4F0R

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.199
R-Value Work: 0.163
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 / NBRC 12614 / NCIMB 9131 / NCTC 9757)) Explore Q7NZ90 Go to UniProtKB: Q7NZ90
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7NZ90
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MTA Query on MTA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	5'-DEOXY-5'-METHYLTHIOADENOSINE C₁₁ H₁₅ N₅ O₃ S WUUGFSXJNOTRMR-IOSLPCCCSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.163
R-Value Observed: 0.165
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-06-06

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

4F0R

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)