4DZH

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.233
R-Value Work: 0.208
R-Value Observed: 0.209

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 51.89 kDa
Atom Count: 3,673
Modelled Residue Count: 439
Deposited Residue Count: 472
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8P8H1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A]	E [auth A], F [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
UNL Query on UNL Download Ideal Coordinates CCD File	G [auth A]	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.233
R-Value Work: 0.208
R-Value Observed: 0.209
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-03-21

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

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