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), 0.220 (DCC)
R-Value Work:
0.212 (Depositor), 0.210 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 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 O [auth A] 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 J [auth A] SDF format, chain IA [auth C] SDF format, chain I [auth A] SDF format, chain HA [auth C] SDF format, chain GA [auth C] SDF format, chain FA [auth C] SDF format, chain EA [auth C] SDF format, chain DA [auth C] SDF format, chain CB [auth F] SDF format, chain CA [auth C] 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 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 O [auth A] 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 J [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CB [auth F] MOL2 format, chain CA [auth C] 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 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 O [auth A] 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 J [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain CB [auth F] mmCIF format, chain CA [auth C] 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]