4JXN

CRYSTAL STRUCTURE OF POLYPRENYL SYNTHASE ISP_B (TARGET EFI-509198) FROM Roseobacter denitrificans

PDB DOI: https://doi.org/10.2210/pdb4JXN/pdb

Classification: TRANSFERASE
Organism(s): Roseobacter denitrificans OCh 114
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-03-28 Released: 2013-05-01
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: 0.283
R-Value Work: 0.218
R-Value Observed: 0.220

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 Isp_B from Roseobacter Denitrificans

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: 36.16 kDa
Atom Count: 2,297
Modelled Residue Count: 297
Deposited Residue Count: 334
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Octaprenyl-diphosphate synthase	A	334	Roseobacter denitrificans OCh 114	Mutation(s): 0 Gene Names: ispB, RD1_3401
UniProt
Find proteins for Q163F0 (Roseobacter denitrificans (strain ATCC 33942 / OCh 114)) Explore Q163F0 Go to UniProtKB: Q163F0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q163F0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
UNL Query on UNL Download Ideal Coordinates CCD File	B [auth A]	Unknown ligand VEXZGXHMUGYJMC-UHFFFAOYSA-M		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: 0.283
R-Value Work: 0.218
R-Value Observed: 0.220
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.49	α = 90
b = 115.172	β = 90
c = 136.221	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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Entry History

Deposition Data

Released Date: 2013-05-01

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2013-05-01
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

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4JXN

CRYSTAL STRUCTURE OF POLYPRENYL SYNTHASE ISP_B (TARGET EFI-509198) FROM Roseobacter denitrificans

Crystal Structure of Isoprenoid Synthase Isp_B from Roseobacter Denitrificans

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)