4JYX | pdb_00004jyx

Crystal structure of polyprenyl synthase PATL_3739 (TARGET EFI-509195) FROM PSEUDOALTEROMONAS ATLANTICA, COMPLEX WITH INORGANIC PHOSPHATE AND AN UNKNOWN LIGAND

PDB DOI: https://doi.org/10.2210/pdb4JYX/pdb

Classification: TRANSFERASE
Organism(s): Paraglaciecola sp. T6c
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-04-01 Released: 2013-04-10
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Poulter, C.D., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.239 (Depositor), 0.243 (DCC)
R-Value Work:
0.177 (Depositor), 0.185 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Isoprenoid Synthase Patl_3739 from Pseudoalteromonas Atlantica

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Poulter, C.D., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 307.61 kDa
Atom Count: 20,169
Modeled Residue Count: 2,511
Deposited Residue Count: 2,760
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trans-hexaprenyltranstransferase	A, B, C, D, E A, B, C, D, E, F, G, H	345	Paraglaciecola sp. T6c	Mutation(s): 0 Gene Names: Patl_3739 EC: 2.5.1.30

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain S [auth F] SDF format, chain T [auth G] SDF format, chain U [auth G] SDF format, chain W [auth H] SDF format, chain X [auth H] SDF format, chain R [auth E] SDF format, chain Q [auth D] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth F] MOL2 format, chain T [auth G] MOL2 format, chain U [auth G] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth F] mmCIF format, chain T [auth G] mmCIF format, chain U [auth G] mmCIF format, chain W [auth H] mmCIF format, chain X [auth H] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain J [auth A]	I [auth A] J [auth A] K [auth A] M [auth B] N [auth B] I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], P [auth C], Q [auth D], R [auth E], S [auth F], T [auth G], U [auth G], W [auth H], X [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth G] Focus chain W [auth H] Focus chain X [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth G] Focus chain W [auth H] Focus chain X [auth H]
UNL Query on UNL Download:Ideal Coordinates CCD File	L [auth A], O [auth B], V [auth G], Y [auth H]	Unknown ligand NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain L [auth A] Focus chain O [auth B] Focus chain V [auth G] Focus chain Y [auth H] Interactions & Density Focus chain L [auth A] Focus chain O [auth B] Focus chain V [auth G] Focus chain Y [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.239 (Depositor), 0.243 (DCC)
R-Value Work: 0.177 (Depositor), 0.185 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.104	α = 90
b = 152.907	β = 90
c = 284.364	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-04-10

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2013-04-10
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description