8K1W | pdb_00008k1w

Crystal structure of PLA2 from Saccharothrix espanaensis

PDB DOI: https://doi.org/10.2210/pdb8K1W/pdb

Classification: HYDROLASE
Organism(s): Saccharothrix espanaensis DSM 44229
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-07-11 Released: 2024-07-24
Deposition Author(s): Zhang, Z.M., Wang, F.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.157 (Depositor), 0.155 (DCC)
R-Value Work:
0.153 (Depositor), 0.150 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: in silico
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of PLA2 from Saccharothrix espanaensis

Zhang, Z.M.

To be published.

Macromolecule Content

Total Structure Weight: 14.47 kDa
Atom Count: 1,120
Modeled Residue Count: 120
Deposited Residue Count: 125
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLA2	A	125	Saccharothrix espanaensis DSM 44229	Mutation(s): 0 Gene Names: BN6_69480
UniProt
Find proteins for K0KBJ2 (Saccharothrix espanaensis (strain ATCC 51144 / DSM 44229 / JCM 9112 / NBRC 15066 / NRRL 15764)) Explore K0KBJ2 Go to UniProtKB: K0KBJ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K0KBJ2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.157 (Depositor), 0.155 (DCC)
R-Value Work: 0.153 (Depositor), 0.150 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.741	α = 90
b = 37.679	β = 90
c = 84.557	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-07-24
Type: Initial release
Version 1.1: 2024-10-16
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.