3SR7 | pdb_00003sr7

Crystal structure of S. mutans isopentenyl pyrophosphate isomerase

PDB DOI: https://doi.org/10.2210/pdb3SR7/pdb

Classification: ISOMERASE
Organism(s): Streptococcus mutans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-07-07 Released: 2012-07-11
Deposition Author(s): Liu, Y.H., Fu, T.M., Liu, X., Su, X.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.285 (Depositor), 0.250 (DCC)
R-Value Work:
0.235 (Depositor), 0.240 (DCC)
R-Value Observed:
0.237 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of S. mutans isopentenyl pyrophosphate isomerase

Liu, Y.H., Fu, T.M., Liu, X., Su, X.D.

To be published.

Macromolecule Content

Total Structure Weight: 163.73 kDa
Atom Count: 8,467
Modeled Residue Count: 1,078
Deposited Residue Count: 1,460
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isopentenyl-diphosphate delta-isomerase	A, B, C, D	365	Streptococcus mutans	Mutation(s): 0 Gene Names: fni, SMU_939 EC: 5.3.3.2
UniProt
Find proteins for Q8DUI9 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DUI9 Go to UniProtKB: Q8DUI9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DUI9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C] mmCIF format, chain E [auth C]	E [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.285 (Depositor), 0.250 (DCC)
R-Value Work: 0.235 (Depositor), 0.240 (DCC)
R-Value Observed: 0.237 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.69	α = 90
b = 76.42	β = 102.21
c = 92.53	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SHELXS	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-07-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-07-11
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.