3WE9 | pdb_00003we9

The crystal structure of YisP from Bacillus subtilis subsp. subtilis strain 168

PDB DOI: https://doi.org/10.2210/pdb3WE9/pdb

Classification: TRANSFERASE
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-07-02 Released: 2014-07-02
Deposition Author(s): Hu, Y., Huang, C.H., Chan, H.C., Ko, T.P., Feng, X., Oldfield, E., Guo, R.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.233 (Depositor), 0.220 (DCC)
R-Value Work:
0.211 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Bacillus subtilis YisP in complex with a PEG fragment

Hu, Y., Huang, C.H., Chan, H.C., Ko, T.P., Feng, X., Oldfield, E., Guo, R.T.

To be published.

Macromolecule Content

Total Structure Weight: 31.7 kDa
Atom Count: 2,235
Modeled Residue Count: 247
Deposited Residue Count: 274
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phytoene/squalene synthase YisP	A	274	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: yisP, yucD, BSU10810 EC: 2.5.1 (PDB Primary Data), 3.1.7.6 (UniProt)
UniProt
Find proteins for O06728 (Bacillus subtilis (strain 168)) Explore O06728 Go to UniProtKB: O06728
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O06728
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE 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]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-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: 1.92 Å
R-Value Free: 0.233 (Depositor), 0.220 (DCC)
R-Value Work: 0.211 (Depositor), 0.210 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.966	α = 90
b = 77.576	β = 90
c = 91.378	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
RESOLVE	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
RESOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-07-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-07-02
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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.