3C3M | pdb_00003c3m

Crystal structure of the N-terminal domain of response regulator receiver protein from Methanoculleus marisnigri JR1

• PDB DOI: https://doi.org/10.2210/pdb3C3M/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Methanoculleus marisnigri JR1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-01-28 Released: 2008-02-05 
• Deposition Author(s): Patskovsky, Y., Ramagopal, U.A., Toro, R., Meyer, A.J., Dickey, M., Chang, S., Groshong, C., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.193 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

Crystal structure of the N-terminal domain of response regulator receiver protein from Methanoculleus marisnigri JR1.

Patskovsky, Y., Ramagopal, U.A., Toro, R., Meyer, A.J., Dickey, M., Chang, S., Groshong, C., Sauder, J.M., Burley, S.K., 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 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.23 kDa 
• Atom Count: 1,230 
• Modeled Residue Count: 123 
• Deposited Residue Count: 138 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator receiver protein	A	138	Methanoculleus marisnigri JR1	Mutation(s): 0  Gene Names: Memar_0295, Memar_0309
UniProt
Find proteins for A3CS79 (Methanoculleus marisnigri (strain ATCC 35101 / DSM 1498 / JR1)) Explore A3CS79  Go to UniProtKB:  A3CS79

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.70 Å
• R-Value Free:  0.193 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.744	α = 90
b = 57.744	β = 90
c = 93.233	γ = 120

Software Package:

Software Name	Purpose
SHELXD	phasing
SHELXE	model building
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-05 
Deposition Author(s): Patskovsky, Y., Ramagopal, U.A., Toro, R., Meyer, A.J., Dickey, M., Chang, S., Groshong, C., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-02-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-10-30
  Changes: Data collection, Database references, Structure summary