3L2H

Crystal structure of Putative sugar phosphate isomerase (AFE_0303) from Acidithiobacillus ferrooxidans ATCC 23270 at 1.85 A resolution

PDB DOI: https://doi.org/10.2210/pdb3L2H/pdb

Classification: ISOMERASE
Organism(s): Acidithiobacillus ferrooxidans ATCC 23270
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-12-15 Released: 2009-12-29
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.180 (Depositor), 0.190 (DCC)
R-Value Observed:
0.181 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Putative sugar phosphate isomerase (AFE_0303) from Acidithiobacillus ferrooxidans ATCC 23270 at 1.85 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 75.92 kDa
Atom Count: 6,227
Modelled Residue Count: 631
Deposited Residue Count: 648
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative sugar phosphate isomerase	A, B, C, D	162	Acidithiobacillus ferrooxidans ATCC 23270	Mutation(s): 0 Gene Names: AFE_0303, AFE_2805
UniProt
Find proteins for B7J8Z8 (Acidithiobacillus ferrooxidans (strain ATCC 23270 / DSM 14882 / CIP 104768 / NCIMB 8455)) Explore B7J8Z8 Go to UniProtKB: B7J8Z8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B7J8Z8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CXS Query on CXS Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain T [auth C] SDF format, chain W [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D]	G [auth A], L [auth B], T [auth C], W [auth D]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C₉ H₁₉ N O₃ S PJWWRFATQTVXHA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain T [auth C] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain T [auth C] Focus chain W [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain Y [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain X [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain X [auth D]	H [auth A] I [auth A] J [auth A] M [auth B] N [auth B] H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], U [auth C], V [auth C], X [auth D], Y [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Y [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	E [auth A], F [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.210 (Depositor), 0.210 (DCC)
R-Value Work: 0.180 (Depositor), 0.190 (DCC)
R-Value Observed: 0.181 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33L2H

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.876	α = 90
b = 93.744	β = 90
c = 139.042	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
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-12-29

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-12-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-06
Changes: Data collection, Refinement description, Structure summary