3JX8 | pdb_00003jx8

Crystal structure of Putative lipid binding protein (YP_001304415.1) from Parabacteroides distasonis ATCC 8503 at 2.16 A resolution

PDB DOI: https://doi.org/10.2210/pdb3JX8/pdb

Classification: CELL ADHESION
Organism(s): Parabacteroides distasonis ATCC 8503
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-09-18 Released: 2009-11-10
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.210 (Depositor), 0.207 (DCC)
R-Value Work:
0.187 (Depositor), 0.186 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Putative lipid binding protein (YP_001304415.1) from Parabacteroides distasonis ATCC 8503 at 2.16 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 166.72 kDa
Atom Count: 13,274
Modeled Residue Count: 1,481
Deposited Residue Count: 1,500
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative lipoprotein	A, B, C, D, E A, B, C, D, E, F	250	Parabacteroides distasonis ATCC 8503	Mutation(s): 0 Gene Names: BDI_3087, YP_001304415.1
UniProt
Find proteins for A6LGH9 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LGH9 Go to UniProtKB: A6LGH9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6LGH9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain RA [auth F] SDF format, chain R [auth B] SDF format, chain QA [auth F] SDF format, chain Q [auth B] SDF format, chain PA [auth F] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain LA [auth E] SDF format, chain KA [auth E] SDF format, chain JA [auth E] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain G [auth A] SDF format, chain FA [auth D] SDF format, chain EA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain RA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain LA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain RA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain LA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain EA [auth D]	EA [auth D] FA [auth D] G [auth A] GA [auth D] H [auth A] EA [auth D], FA [auth D], G [auth A], GA [auth D], H [auth A], I [auth A], JA [auth E], KA [auth E], LA [auth E], N [auth B], O [auth B], P [auth B], PA [auth F], Q [auth B], QA [auth F], R [auth B], RA [auth F], X [auth C], Y [auth C], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain UA [auth F] SDF format, chain U [auth B] SDF format, chain TA [auth F] SDF format, chain T [auth B] SDF format, chain SA [auth F] SDF format, chain OA [auth E] SDF format, chain NA [auth E] SDF format, chain MA [auth E] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IA [auth D] SDF format, chain HA [auth D] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain OA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain OA [auth E] mmCIF format, chain NA [auth E] mmCIF format, chain MA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] HA [auth D] AA [auth C], BA [auth C], CA [auth C], DA [auth C], HA [auth D], IA [auth D], J [auth A], K [auth A], L [auth A], M [auth A], MA [auth E], NA [auth E], OA [auth E], SA [auth F], T [auth B], TA [auth F], U [auth B], UA [auth F], V [auth B], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth F] Focus chain V [auth B] Focus chain W [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.210 (Depositor), 0.207 (DCC)
R-Value Work: 0.187 (Depositor), 0.186 (DCC)
R-Value Observed: 0.189 (Depositor)

Diffraction Data:

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.88	α = 90
b = 201.88	β = 90
c = 202.84	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
autoSHARP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-11-10

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-11-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-10-16
Changes: Data collection, Refinement description, Structure summary