4DZH | pdb_00004dzh

Crystal structure of an adenosine deaminase from xanthomonas campestris (target nysgrc-200456) with bound zn

• PDB DOI: https://doi.org/10.2210/pdb4DZH/pdb

• Classification: HYDROLASE
• Organism(s): Xanthomonas campestris pv. campestris str. ATCC 33913
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-01 Released: 2012-03-21 
• Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Sojitra, S., Chamala, S., Kar, A., Lafleur, J., Villigas, G., Evans, B., Hammonds, J., Gizzi, A., Zencheck, W.D., Hillerich, B., Love, J., Seidel, R.D., Bonanno, J.B., Raushel, F.M., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.233 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an adenosine deaminase from xanthomonas campestris (target nysgrc-200456) with bound zn

Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Sojitra, S., Chamala, S., Kar, A., Lafleur, J., Villigas, G., Evans, B., Hammonds, J., Gizzi, A., Zencheck, W.D., Hillerich, B., Love, J., Seidel, R.D., Bonanno, J.B., Raushel, F.M., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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: 51.89 kDa 
• Atom Count: 3,673 
• Modeled Residue Count: 439 
• Deposited Residue Count: 472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AMIDOHYDROLASE	A	472	Xanthomonas campestris pv. campestris str. ATCC 33913	Mutation(s): 0  Gene Names: XCC2270
UniProt
Find proteins for Q8P8H1 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8P8H1  Go to UniProtKB:  Q8P8H1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A], F [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL	G [auth A]	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.233 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.645	α = 90
b = 53.15	β = 106.54
c = 67.39	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Sojitra, S., Chamala, S., Kar, A., Lafleur, J., Villigas, G., Evans, B., Hammonds, J., Gizzi, A., Zencheck, W.D., Hillerich, B., Love, J., Seidel, R.D., Bonanno, J.B., Raushel, F.M., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description