2QW5 | pdb_00002qw5

CRYSTAL STRUCTURE OF A PUTATIVE SUGAR PHOSPHATE ISOMERASE/EPIMERASE (AVA4194) FROM ANABAENA VARIABILIS ATCC 29413 AT 1.78 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2QW5/pdb

• Classification: ISOMERASE
• Organism(s): Trichormus variabilis ATCC 29413
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-08-09 Released: 2007-09-04 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Crystal structure of putative sugar phosphate isomerase/epimerase (YP_324688.1) from Anabaena variabilis ATCC 29413 at 1.78 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 77.31 kDa 
• Atom Count: 6,066 
• Modelled Residue Count: 652 
• Deposited Residue Count: 670 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase-like TIM barrel	A, B	335	Trichormus variabilis ATCC 29413	Mutation(s): 0  Gene Names: YP_324688.1, Ava_4194
UniProt
Find proteins for Q3M5E3 (Trichormus variabilis (strain ATCC 29413 / PCC 7937)) Explore Q3M5E3  Go to UniProtKB:  Q3M5E3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XLS	C [auth A], I [auth B]	D-xylose C5 H10 O5 PYMYPHUHKUWMLA-VPENINKCSA-N
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	E [auth A], F [auth A], G [auth A], K [auth B], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.78 Å
• R-Value Free:  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32QW5

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.238	α = 90
b = 84.238	β = 90
c = 208.172	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-04 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-09-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Advisory, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 1.5: 2023-01-25
  Changes: Database references, Structure summary
• Version 1.6: 2024-11-13
  Changes: Data collection, Structure summary