4Q82 | pdb_00004q82

Crystal Structure of Phospholipase/Carboxylesterase from Haliangium ochraceum

• PDB DOI: https://doi.org/10.2210/pdb4Q82/pdb

• Classification: HYDROLASE
• Organism(s): Haliangium ochraceum DSM 14365
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-25 Released: 2014-05-14 
• Deposition Author(s): Kim, Y., Hatzos-Skintges, C., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.175 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

Crystal Structure of Phospholipase/Carboxylesterase from Haliangium ochraceum

Kim, Y., Hatzos-Skintges, C., Endres, M., 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: 59.83 kDa 
• Atom Count: 4,204 
• Modeled Residue Count: 469 
• Deposited Residue Count: 554 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase/Carboxylesterase	A, B	277	Haliangium ochraceum DSM 14365	Mutation(s): 0  Gene Names: Hoch_6203
UniProt
Find proteins for D0LMJ0 (Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2)) Explore D0LMJ0  Go to UniProtKB:  D0LMJ0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	H [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A], G [auth B], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2ZC	A, B	L-PEPTIDE LINKING	C11 H16 N2 O5 S		SER
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.175 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.935	α = 90
b = 146.084	β = 90
c = 68.72	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
DM	model building
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): Kim, Y., Hatzos-Skintges, C., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Experimental preparation
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary