7WU1 | pdb_00007wu1

Crystal structure of phospholipase D from Moritella sp. JT01

PDB DOI: https://doi.org/10.2210/pdb7WU1/pdb

Classification: HYDROLASE
Organism(s): Moritella sp. JT01
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-02-05 Released: 2023-02-08
Deposition Author(s): Wang, Y.H., Mao, X.J., Wang, J., Wang, F.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.216 (Depositor), 0.217 (DCC)
R-Value Work:
0.212 (Depositor), 0.213 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7WU1

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of phospholipase D from Moritella sp. JT01

Wang, Y.H., Mao, X.J., Wang, J., Wang, F.H.

To be published.

Macromolecule Content

Total Structure Weight: 373.17 kDa
Atom Count: 26,491
Modeled Residue Count: 3,254
Deposited Residue Count: 3,342
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase D	A, B, C, D, E A, B, C, D, E, F	557	Moritella sp. JT01	Mutation(s): 0 Gene Names: AKG98_3441 EC: 3.1.4.4
UniProt
Find proteins for A0ACD6B9Z1 (Moritella sp. JT01) Explore A0ACD6B9Z1 Go to UniProtKB: A0ACD6B9Z1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B9Z1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain EA [auth C] SDF format, chain HA [auth C] SDF format, chain J [auth A] SDF format, chain O [auth A] SDF format, chain ZA [auth F] SDF format, chain Z [auth B] SDF format, chain YA [auth F] SDF format, chain Y [auth B] SDF format, chain XA [auth F] SDF format, chain X [auth B] SDF format, chain WA [auth E] SDF format, chain W [auth B] SDF format, chain VA [auth E] SDF format, chain V [auth B] SDF format, chain UA [auth E] SDF format, chain U [auth B] SDF format, chain TA [auth D] SDF format, chain T [auth B] SDF format, chain SA [auth D] SDF format, chain S [auth B] SDF format, chain RA [auth D] SDF format, chain R [auth B] SDF format, chain QA [auth D] SDF format, chain Q [auth A] SDF format, chain PA [auth D] SDF format, chain P [auth A] SDF format, chain OA [auth D] SDF format, chain NA [auth D] SDF format, chain N [auth A] SDF format, chain MA [auth D] SDF format, chain M [auth A] SDF format, chain LA [auth C] SDF format, chain L [auth A] SDF format, chain KA [auth C] SDF format, chain K [auth A] SDF format, chain JA [auth C] SDF format, chain IA [auth C] SDF format, chain I [auth A] SDF format, chain GA [auth C] SDF format, chain FA [auth C] SDF format, chain DA [auth C] SDF format, chain CB [auth F] SDF format, chain BB [auth F] SDF format, chain BA [auth C] SDF format, chain AB [auth F] SDF format, chain AA [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain O [auth A] MOL2 format, chain ZA [auth F] MOL2 format, chain Z [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain Y [auth B] MOL2 format, chain XA [auth F] MOL2 format, chain X [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CB [auth F] MOL2 format, chain BB [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain AB [auth F] MOL2 format, chain AA [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain O [auth A] mmCIF format, chain ZA [auth F] mmCIF format, chain Z [auth B] mmCIF format, chain YA [auth F] mmCIF format, chain Y [auth B] mmCIF format, chain XA [auth F] mmCIF format, chain X [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain CB [auth F] mmCIF format, chain BB [auth F] mmCIF format, chain BA [auth C] mmCIF format, chain AB [auth F] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth F] BA [auth C] BB [auth F] CA [auth C] AA [auth B], AB [auth F], BA [auth C], BB [auth F], CA [auth C], CB [auth F], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], Q [auth A], QA [auth D], R [auth B], RA [auth D], S [auth B], SA [auth D], T [auth B], TA [auth D], U [auth B], UA [auth E], V [auth B], VA [auth E], W [auth B], WA [auth E], X [auth B], XA [auth F], Y [auth B], YA [auth F], Z [auth B], ZA [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain CB [auth F] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth F] Focus chain Y [auth B] Focus chain YA [auth F] Focus chain Z [auth B] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain BB [auth F] Focus chain CA [auth C] Focus chain CB [auth F] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth F] Focus chain Y [auth B] Focus chain YA [auth F] Focus chain Z [auth B] Focus chain ZA [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.216 (Depositor), 0.217 (DCC)
R-Value Work: 0.212 (Depositor), 0.213 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.897	α = 90
b = 216.644	β = 90
c = 277.708	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31725022
National Natural Science Foundation of China (NSFC)	China	31972014

Revision History (Full details and data files)

Version 1.0: 2023-02-08
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
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.