2ZE4 | pdb_00002ze4

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 (Depositor), 0.169 (DCC)
R-Value Work:
0.121 (Depositor), 0.120 (DCC)
R-Value Observed:
0.124 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.2 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
Modeled Residue Count: 501
Deposited Residue Count: 509
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.169 (DCC)
R-Value Work: 0.121 (Depositor), 0.120 (DCC)
R-Value Observed: 0.124 (Depositor)

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

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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
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, 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.