8GXV | pdb_00008gxv

Structure of a bacterial serpin Choloropin derived from Cholorobium limicola

• PDB DOI: https://doi.org/10.2210/pdb8GXV/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Chlorobium limicola DSM 245
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-21 Released: 2023-09-27 
• Deposition Author(s): Zhou, A., Xu, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.248 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Climpin, a Novel Bacterial a Serpin inducing a Broad Range of Proteases and Regulated by Heparin and DNA.

Zhou, A., Xu, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.04 kDa 
• Atom Count: 2,852 
• Modeled Residue Count: 353 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteinase inhibitor I4 serpin	A	375	Chlorobium limicola DSM 245	Mutation(s): 0  Gene Names: Clim_1363
UniProt
Find proteins for B3ECZ8 (Chlorobium limicola (strain DSM 245 / NBRC 103803 / 6330)) Explore B3ECZ8  Go to UniProtKB:  B3ECZ8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.248 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.66	α = 90
b = 60.91	β = 90
c = 130.16	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
Coot	model building
REFMAC	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-27 
Deposition Author(s): Zhou, A., Xu, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81870309
National Natural Science Foundation of China (NSFC)	China	32070934

Revision History  

• Version 1.0: 2023-09-27
  Type: Initial release
  
• Version 1.1: 2026-03-11
  Changes: Refinement description, Structure summary