3HBA

Crystal structure of a putative phosphosugar isomerase (sden_2705) from shewanella denitrificans os217 at 2.00 A resolution

PDB DOI: https://doi.org/10.2210/pdb3HBA/pdb

Classification: ISOMERASE
Organism(s): Shewanella denitrificans OS217
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-04 Released: 2009-05-19
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.203
R-Value Work: 0.165
R-Value Observed: 0.167

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Putative phosphosugar isomerase (YP_563707.1) from SHEWANELLA DENITRIFICANS OS-217 at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 71.92 kDa
Atom Count: 5,171
Modelled Residue Count: 623
Deposited Residue Count: 668
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 phosphosugar isomerase	A, B	334	Shewanella denitrificans OS217	Mutation(s): 0 Gene Names: Sden_2705, YP_563707.1 EC: 2.6.1.16
UniProt
Find proteins for Q12KP2 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)) Explore Q12KP2 Go to UniProtKB: Q12KP2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12KP2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.203
R-Value Work: 0.165
R-Value Observed: 0.167
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M33HBA

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.579	α = 90
b = 89.445	β = 90
c = 109.497	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

Entry History

Deposition Data

Released Date: 2009-05-19

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-05-19
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

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3HBA

Crystal structure of a putative phosphosugar isomerase (sden_2705) from shewanella denitrificans os217 at 2.00 A resolution

Crystal structure of Putative phosphosugar isomerase (YP_563707.1) from SHEWANELLA DENITRIFICANS OS-217 at 2.00 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)