3HBA | pdb_00003hba

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.203 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71.92 kDa 
• Atom Count: 5,171 
• Modeled Residue Count: 623 
• Deposited Residue Count: 668 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], E [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33HBA

Space Group: P 2₁ 2₁ 2₁

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

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.5: 2024-11-27
  Changes: Data collection, Refinement description, Structure summary