4Q7Q | pdb_00004q7q

The crystal structure of a possible lipase from Chitinophaga pinensis DSM 2588

• PDB DOI: https://doi.org/10.2210/pdb4Q7Q/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Chitinophaga pinensis DSM 2588
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-25 Released: 2014-05-14 
• Deposition Author(s): Tan, K., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.190 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Literature

The crystal structure of a possible lipase from Chitinophaga pinensis DSM 2588

Tan, K., Tesar, C., Clancy, S., Joachimiak, A.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.48 kDa 
• Atom Count: 4,595 
• Modeled Residue Count: 516 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipolytic protein G-D-S-L family	A, B	266	Chitinophaga pinensis DSM 2588	Mutation(s): 0  Gene Names: Cpin_6674

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
FMT	E [auth A], G [auth B], H [auth B], I [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.190 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.611	α = 90
b = 80.611	β = 90
c = 93.005	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
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-14 
Deposition Author(s): Tan, K., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary