4JWO

The crystal structure of a possible phosphate binding protein from Planctomyces limnophilus DSM 3776

PDB DOI: https://doi.org/10.2210/pdb4JWO/pdb

Classification: Phosphate binding protein
Organism(s): Planctopirus limnophila DSM 3776
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-03-27 Released: 2013-04-24
Deposition Author(s): Tan, K., Gu, M., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.195 (Depositor), 0.199 (DCC)
R-Value Work:
0.172 (Depositor), 0.173 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of a possible phosphate binding protein from Planctomyces limnophilus DSM 3776

Tan, K., Gu, M., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 37.58 kDa
Atom Count: 2,519
Modelled Residue Count: 284
Deposited Residue Count: 341
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphate binding protein	A	341	Planctopirus limnophila DSM 3776	Mutation(s): 0 Gene Names: Plim_1490
UniProt
Find proteins for D5SW38 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)) Explore D5SW38 Go to UniProtKB: D5SW38
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D5SW38
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.195 (Depositor), 0.199 (DCC)
R-Value Work: 0.172 (Depositor), 0.173 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.158	α = 90
b = 87.158	β = 90
c = 75.536	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-04-24

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-04-24
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary