2ZE9 | pdb_00002ze9

Crystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholine

PDB DOI: https://doi.org/10.2210/pdb2ZE9/pdb

Classification: HYDROLASE
Organism(s): Streptomyces antibioticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-12-06 Released: 2007-12-25
Deposition Author(s): Suzuki, A., Toda, H., Iwasaki, Y., Yamane, T., Yamane, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.251 (Depositor), 0.180 (DCC)
R-Value Work:
0.170 (Depositor), 0.174 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of phospholipase D from streptomyces antibioticus.

Suzuki, A., Toda, H., Iwasaki, Y., Yamane, T., Yamane, T.

To be published.

Macromolecule Content

Total Structure Weight: 54.56 kDa
Atom Count: 4,161
Modeled Residue Count: 504
Deposited Residue Count: 509
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase D	A	509	Streptomyces antibioticus	Mutation(s): 1 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PD7 Query on PD7 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(2R)-3-(phosphonooxy)propane-1,2-diyl diheptanoate C₁₇ H₃₃ O₈ P JAXUAGQDLYDLQB-OAHLLOKOSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
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: 2.30 Å
R-Value Free: 0.251 (Depositor), 0.180 (DCC)
R-Value Work: 0.170 (Depositor), 0.174 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.868	α = 90
b = 78.232	β = 90
c = 98.603	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
DENZO	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2023-11-01
Changes: Data collection, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary
Version 1.5: 2025-04-30
Changes: Database references

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.