3MR7 | pdb_00003mr7

Crystal Structure of Adenylate/Guanylate Cyclase/Hydrolase from Silicibacter pomeroyi

PDB DOI: https://doi.org/10.2210/pdb3MR7/pdb

Classification: HYDROLASE
Organism(s): Ruegeria pomeroyi DSS-3
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-04-28 Released: 2010-06-23
Deposition Author(s): Kim, Y., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.246 (Depositor), 0.244 (DCC)
R-Value Work:
0.177 (Depositor), 0.178 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Adenylate/Guanylate Cyclase/Hydrolase from Silicibacter pomeroyi

Kim, Y., Li, H., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 64.32 kDa
Atom Count: 4,112
Modelled Residue Count: 514
Deposited Residue Count: 567
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate/guanylate cyclase/hydrolase, alpha/beta fold family	A, B, C	189	Ruegeria pomeroyi DSS-3	Mutation(s): 0 Gene Names: SPO3024
UniProt
Find proteins for Q5LP28 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LP28 Go to UniProtKB: Q5LP28
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5LP28
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.246 (Depositor), 0.244 (DCC)
R-Value Work: 0.177 (Depositor), 0.178 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.106	α = 90
b = 97.106	β = 90
c = 216.743	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-06-23

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-06-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.