3N53 | pdb_00003n53

Crystal structure of a response regulator receiver modulated diguanylate cyclase from Pelobacter carbinolicus

• PDB DOI: https://doi.org/10.2210/pdb3N53/pdb

• Classification: TRANSCRIPTION
• Organism(s): Syntrophotalea carbinolica DSM 2380
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-24 Released: 2010-07-28 
• Deposition Author(s): Palani, K., Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.286 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a response regulator receiver modulated diguanylate cyclase from Pelobacter carbinolicus

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33 kDa 
• Atom Count: 1,780 
• Modeled Residue Count: 210 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator receiver modulated diguanylate cyclase	A, B	140	Syntrophotalea carbinolica DSM 2380	Mutation(s): 0  Gene Names: Pcar_0634 EC: 2.7.7.65
UniProt
Find proteins for Q3A6W4 (Syntrophotalea carbinolica (strain DSM 2380 / NBRC 103641 / GraBd1)) Explore Q3A6W4  Go to UniProtKB:  Q3A6W4

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.286 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.004	α = 90
b = 44.932	β = 94.37
c = 88.681	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Palani, K., Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-07-28
  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