3GYD | pdb_00003gyd

Crystal structure of a cyclic nucleotide-binding domain (mfla_1926) from methylobacillus flagellatus kt at 1.79 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3GYD/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Methylobacillus flagellatus KT
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-03 Released: 2009-04-21 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.212 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Crystal structure of cyclic nucleotide-binding domain (YP_546034.1) from Methylobacillus flagellatus KT at 1.79 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.39 kDa 
• Atom Count: 3,215 
• Modeled Residue Count: 358 
• Deposited Residue Count: 374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic nucleotide-binding domain	A, B	187	Methylobacillus flagellatus KT	Mutation(s): 0  Gene Names: Mfla_1926, YP_546034.1
UniProt
Find proteins for Q1GZZ4 (Methylobacillus flagellatus (strain ATCC 51484 / DSM 6875 / VKM B-1610 / KT)) Explore Q1GZZ4  Go to UniProtKB:  Q1GZZ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMP	C [auth A], D [auth B]	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE C10 H12 N5 O6 P IVOMOUWHDPKRLL-KQYNXXCUSA-N
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 1.79 Å
• R-Value Free:  0.212 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33GYD

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.032	α = 90
b = 39.745	β = 101.85
c = 70.977	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary