2RD9 | pdb_00002rd9

Crystal structure of a putative yfit-like metal-dependent hydrolase (bh0186) from bacillus halodurans c-125 at 2.30 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2RD9/pdb

• Classification: HYDROLASE
• Organism(s): Halalkalibacterium halodurans C-125
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-09-21 Released: 2007-10-09 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.201 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Literature

Crystal structure of YfiT-like putative metal-dependent hydrolase (NP_241052.1) from Bacillus halodurans at 2.30 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

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

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 92.79 kDa 
• Atom Count: 6,934 
• Modeled Residue Count: 748 
• Deposited Residue Count: 772 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BH0186 protein	A, B, C, D	193	Halalkalibacterium halodurans C-125	Mutation(s): 0  Gene Names: NP_241052.1, BH0186
UniProt
Find proteins for Q9KGB8 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KGB8  Go to UniProtKB:  Q9KGB8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth A], J [auth A], K [auth A], M [auth B], Q [auth C], S [auth D], T [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	F [auth A], G [auth A], H [auth A], O [auth C], P [auth C]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
NI	E [auth A], L [auth B], N [auth C], R [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

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: 2.30 Å
• R-Value Free:  0.201 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32RD9

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.33	α = 90
b = 147.33	β = 90
c = 147.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-09 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-10-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-09
  Changes: Data collection, Refinement description, Structure summary