4HCJ | pdb_00004hcj

Crystal Structure of ThiJ/PfpI Domain Protein from Brachyspira murdochii

• PDB DOI: https://doi.org/10.2210/pdb4HCJ/pdb

• Classification: HYDROLASE
• Organism(s): Brachyspira murdochii DSM 12563
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-09-30 Released: 2012-10-24 
• Deposition Author(s): Kim, Y., Bigelow, L., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 
  0.127 (Depositor), 0.122 (DCC) 
• R-Value Work: 
  0.116 (Depositor), 0.114 (DCC) 
• R-Value Observed: 
  0.116 (Depositor) 

Literature

Crystal Structure of ThiJ/PfpI Domain Protein from Brachyspira murdochii

Kim, Y., Bigelow, L., Jedrzejczak, R., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 19.25 kDa 
• Atom Count: 1,803 
• Modeled Residue Count: 173 
• Deposited Residue Count: 177 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ThiJ/PfpI domain protein	A	177	Brachyspira murdochii DSM 12563	Mutation(s): 0  Gene Names: Bmur_0257
UniProt
Find proteins for D5U596 (Brachyspira murdochii (strain ATCC 51284 / DSM 12563 / 56-150)) Explore D5U596  Go to UniProtKB:  D5U596

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	F [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.12 Å
• R-Value Free:  0.127 (Depositor), 0.122 (DCC) 
• R-Value Work:  0.116 (Depositor), 0.114 (DCC) 
• R-Value Observed: 0.116 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34HCJ

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.799	α = 90
b = 42.197	β = 116.95
c = 66.366	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
ARP/wARP	model building
ahelx-97	refinement
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-24 
Deposition Author(s): Kim, Y., Bigelow, L., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary