2OIK | pdb_00002oik

Crystal structure of a histidine triad (hit) protein (mfla_2506) from methylobacillus flagellatus kt at 1.65 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2OIK/pdb

• Classification: HYDROLASE
• Organism(s): Methylobacillus flagellatus KT
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-01-11 Released: 2007-01-30 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.223 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Crystal structure of histidine triad (HIT) protein (YP_546612.1) from Methylobacillus flagellatus KT at 1.65 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 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 73.38 kDa 
• Atom Count: 4,941 
• Modeled Residue Count: 558 
• Deposited Residue Count: 616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine triad (HIT) protein	A, B, C, D	154	Methylobacillus flagellatus KT	Mutation(s): 8  Gene Names: YP_546612.1, Mfla_2506
UniProt
Find proteins for Q1GYB6 (Methylobacillus flagellatus (strain ATCC 51484 / DSM 6875 / VKM B-1610 / KT)) Explore Q1GYB6  Go to UniProtKB:  Q1GYB6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], P [auth C], Q [auth C], U [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A], J [auth B], N [auth C], R [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth A], K [auth B], O [auth C], S [auth D], T [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.223 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32OIK

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.243	α = 108.13
b = 47.981	β = 98.22
c = 69.766	γ = 90.34

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-30 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-01-30
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary