3HCZ | pdb_00003hcz

The crystal structure of a domain of possible thiol-disulfide isomerase from Cytophaga hutchinsonii ATCC 33406.

• PDB DOI: https://doi.org/10.2210/pdb3HCZ/pdb

• Classification: structural genomics, unknown function
• Organism(s): Cytophaga hutchinsonii ATCC 33406
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-06 Released: 2009-05-19 
• Deposition Author(s): Tan, K., Marshall, N., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.219 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.179 (Depositor) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

The crystal structure of a domain of possible thiol-disulfide isomerase from Cytophaga hutchinsonii ATCC 33406.

Tan, K., Marshall, N., Cobb, G., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.15 kDa 
• Atom Count: 1,423 
• Modeled Residue Count: 147 
• Deposited Residue Count: 148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Possible thiol-disulfide isomerase	A	148	Cytophaga hutchinsonii ATCC 33406	Mutation(s): 0  Gene Names: CHU_0134, Cytophaga hutchinsonii

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FMT	G [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-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: 1.88 Å
• R-Value Free:  0.219 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.179 (Depositor) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.011	α = 90
b = 55.011	β = 90
c = 126.072	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-19 
Deposition Author(s): Tan, K., Marshall, N., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary