4H0C | pdb_00004h0c

Crystal structure of phospholipase/Carboxylesterase from Dyadobacter fermentans DSM 18053

• PDB DOI: https://doi.org/10.2210/pdb4H0C/pdb

• Classification: HYDROLASE
• Organism(s): Dyadobacter fermentans DSM 18053
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-09-07 Released: 2012-09-26 
• Deposition Author(s): Chang, C., Holowicki, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.194 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Literature

Crystal structure of phospholipase/Carboxylesterase from Dyadobacter fermentans DSM 18053

Chang, C., Holowicki, J., 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: 46.25 kDa 
• Atom Count: 3,548 
• Modeled Residue Count: 419 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase/Carboxylesterase	A, B	210	Dyadobacter fermentans DSM 18053	Mutation(s): 0  Gene Names: Dfer_0355
UniProt
Find proteins for C6VYE5 (Dyadobacter fermentans (strain ATCC 700827 / DSM 18053 / CIP 107007 / KCTC 52180 / NS114)) Explore C6VYE5  Go to UniProtKB:  C6VYE5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], E [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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: 1.62 Å
• R-Value Free:  0.194 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34H0C

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.157	α = 72.77
b = 40.251	β = 78.37
c = 67.256	γ = 76.09

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
ARP/wARP	model building
RESOLVE	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-26 
Deposition Author(s): Chang, C., Holowicki, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary