4HGX | pdb_00004hgx

Crystal structure of xylose isomerase domain containing protein (stm4435) from salmonella typhimurium lt2 with unknown ligand

• PDB DOI: https://doi.org/10.2210/pdb4HGX/pdb

• Classification: ISOMERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-09 Released: 2012-10-24 
• Deposition Author(s): Boyko, K.M., Gorbacheva, M.A., Korzhenevskiy, D.A., Dorovatovsky, P.V., Rakitina, T.V., Lipkin, A.V., Shumilin, I.A., Minor, W., Popov, V.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.302 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of xylose isomerase domain containing protein (stm4435) from salmonella typhimurium lt2 with unknown ligand

Boyko, K.M., Gorbacheva, M.A., Korzhenevskiy, D.A., Dorovatovsky, P.V., Rakitina, T.V., Lipkin, A.V., Shumilin, I.A., Minor, W., Popov, V.O.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.87 kDa 
• Atom Count: 4,282 
• Modeled Residue Count: 539 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase domain containing protein	A, B	271	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: STM4435
UniProt
Find proteins for Q8ZK48 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZK48  Go to UniProtKB:  Q8ZK48

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	D [auth A], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.302 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.18	α = 90
b = 93.18	β = 90
c = 125.21	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
AUTOMAR	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-24 
Deposition Author(s): Boyko, K.M., Gorbacheva, M.A., Korzhenevskiy, D.A., Dorovatovsky, P.V., Rakitina, T.V., Lipkin, A.V., Shumilin, I.A., Minor, W., Popov, V.O.

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 1.1: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Refinement description