3HZ6 | pdb_00003hz6

Crystal structure of xylulokinase from Chromobacterium violaceum

• PDB DOI: https://doi.org/10.2210/pdb3HZ6/pdb

• Classification: TRANSFERASE
• Organism(s): Chromobacterium violaceum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-23 Released: 2009-07-21 
• Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.193 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Crystal structure of xylulokinase from Chromobacterium violaceum

Zhang, Z., Burley, S.K., Swaminathan, S.

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)

Macromolecule Content 

• Total Structure Weight: 57.04 kDa 
• Atom Count: 4,394 
• Modeled Residue Count: 497 
• Deposited Residue Count: 511 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylulokinase	A	511	Chromobacterium violaceum	Mutation(s): 0  Gene Names: CV_1862, xylB EC: 2.7.1.17
UniProt
Find proteins for Q7NWW7 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q7NWW7  Go to UniProtKB:  Q7NWW7

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
XUL	G [auth A]	D-XYLULOSE C5 H10 O5 ZAQJHHRNXZUBTE-WUJLRWPWSA-N
MLI	F [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.193 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.512	α = 90
b = 159.427	β = 90
c = 47.185	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-21 
Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Structure summary