2YIJ | pdb_00002yij

Crystal Structure of phospholipase A1

PDB DOI: https://doi.org/10.2210/pdb2YIJ/pdb

Classification: HYDROLASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-05-13 Released: 2012-05-30
Deposition Author(s): Lee, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.264 (Depositor), 0.228 (DCC)
R-Value Work:
0.231 (Depositor), 0.259 (DCC)
R-Value Observed:
0.263 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Phospholipase A1

Lee, I.

To be published.

Macromolecule Content

Total Structure Weight: 96.46 kDa
Atom Count: 6,596
Modeled Residue Count: 776
Deposited Residue Count: 838
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOLIPASE A1-IIGAMMA	A, B	419	Arabidopsis thaliana	Mutation(s): 0 EC: 3.1.1
UniProt
Find proteins for O49523 (Arabidopsis thaliana) Explore O49523 Go to UniProtKB: O49523
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O49523
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.264 (Depositor), 0.228 (DCC)
R-Value Work: 0.231 (Depositor), 0.259 (DCC)
R-Value Observed: 0.263 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.223	α = 90
b = 95.854	β = 105.31
c = 78.891	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-05-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-05-30
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Other, 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.