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), 0.225 (DCC)
R-Value Work:
0.211 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3WE9

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.225 (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

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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

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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.