3K9T

Crystal structure of putative peptidase (NP_348812.1) from CLOSTRIDIUM ACETOBUTYLICUM at 2.37 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3K9T/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium acetobutylicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-16 Released: 2009-11-10 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 0.212 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Literature

Crystal structure of putative peptidase (NP_348812.1) from CLOSTRIDIUM ACETOBUTYLICUM at 2.37 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content

• Total Structure Weight: 51.26 kDa 
• Atom Count: 3,657 
• Modelled Residue Count: 422 
• Deposited Residue Count: 435 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative peptidase	A	435	Clostridium acetobutylicum	Mutation(s): 0  Gene Names: CA_C2195
UniProt
Find proteins for Q97H19 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787)) Explore Q97H19  Go to UniProtKB:  Q97H19

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	F [auth A], G [auth A], H [auth A], I [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
IMD	E [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 2.37 Å
• R-Value Free: 0.212 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: H 3 2
• Diffraction Data: https://doi.org/10.18430/M33K9T

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.782	α = 90
b = 153.782	β = 90
c = 168.378	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-10 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-11-10
  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: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations