4F0R | pdb_00004f0r

Crystal structure of an adenosine deaminase homolog from Chromobacterium violaceum (target NYSGRC-019589) bound Zn and 5'-Methylthioadenosine (unproductive complex)

• PDB DOI: https://doi.org/10.2210/pdb4F0R/pdb

• Classification: HYDROLASE
• Organism(s): Chromobacterium violaceum ATCC 12472
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-04 Released: 2012-06-06 
• Deposition Author(s): Kim, J., Vetting, M.W., Sauder, J.M., Burley, S.K., Raushel, F.M., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.199 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

Crystal structure of an adenosine deaminase homolog from Chromobacterium violaceum (target NYSGRC-019589) bound Zn and 5'-Methylthioadenosine (unproductive complex)

Kim, J., Vetting, M.W., Sauder, J.M., Burley, S.K., Raushel, F.M., Bonanno, J.B., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.66 kDa 
• Atom Count: 3,669 
• Modeled Residue Count: 436 
• Deposited Residue Count: 447 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-methylthioadenosine/S-adenosylhomocysteine deaminase	A	447	Chromobacterium violaceum ATCC 12472	Mutation(s): 0  Gene Names: CV_1032, mtaD EC: 3.5.4.28 (PDB Primary Data), 3.5.4.31 (PDB Primary Data)
UniProt
Find proteins for Q7NZ90 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q7NZ90  Go to UniProtKB:  Q7NZ90

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTA	D [auth A]	5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S WUUGFSXJNOTRMR-IOSLPCCCSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-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: 1.80 Å
• R-Value Free:  0.199 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.152	α = 90
b = 101.152	β = 90
c = 88.623	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-06 
Deposition Author(s): Kim, J., Vetting, M.W., Sauder, J.M., Burley, S.K., Raushel, F.M., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Structure summary