2ZE4

Crystal structure of phospholipase D from streptomyces antibioticus

PDB DOI: https://doi.org/10.2210/pdb2ZE4/pdb

Classification: HYDROLASE
Organism(s): Streptomyces antibioticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-12-05 Released: 2007-12-25
Deposition Author(s): Suzuki, A., Kakuno, K., Saito, R., Iwasaki, Y., Yamane, T., Yamane, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.171
R-Value Work: 0.121
R-Value Observed: 0.124

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of phospholipase D from streptomyces antibioticus

Suzuki, A., Kakuno, K., Saito, R., Iwasaki, Y., Yamane, T., Yamane, T.

To be published.

Macromolecule Content

Total Structure Weight: 54.23 kDa
Atom Count: 3,959
Modelled Residue Count: 501
Deposited Residue Count: 509
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase D	A	509	Streptomyces antibioticus	Mutation(s): 0 EC: 3.1.4.4
UniProt
Find proteins for Q53728 (Streptomyces antibioticus) Explore Q53728 Go to UniProtKB: Q53728
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q53728
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.171
R-Value Work: 0.121
R-Value Observed: 0.124
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.004	α = 90
b = 85.008	β = 90
c = 99.343	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Weissenberg	data collection
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-12-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-12-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.