3KCN | pdb_00003kcn

The crystal structure of adenylate cyclase from Rhodopirellula baltica

PDB DOI: https://doi.org/10.2210/pdb3KCN/pdb

Classification: LYASE
Organism(s): Rhodopirellula baltica
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-10-21 Released: 2009-11-17
Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.267 (Depositor), 0.260 (DCC)
R-Value Work:
0.217 (Depositor), 0.215 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3KCN

This is version 1.5 of the entry. See complete history.

Literature

The crystal structure of adenylate cyclase from Rhodopirellula baltica

Zhang, Z., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 34.57 kDa
Atom Count: 2,244
Modeled Residue Count: 272
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate cyclase homolog	A, B	151	Rhodopirellula baltica	Mutation(s): 0 Gene Names: cyaA, RB11090
UniProt
Find proteins for Q7UJS6 (Rhodopirellula baltica (strain DSM 10527 / NCIMB 13988 / SH1)) Explore Q7UJS6 Go to UniProtKB: Q7UJS6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7UJS6
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.267 (Depositor), 0.260 (DCC)
R-Value Work: 0.217 (Depositor), 0.215 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.93	α = 90
b = 103.096	β = 90
c = 33.867	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-11-17

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-11-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Refinement description
Version 1.4: 2023-11-22
Changes: Data collection
Version 1.5: 2024-11-20
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.