3HYQ | pdb_00003hyq

Crystal Structure of Isopentenyl-Diphosphate delta-Isomerase from Salmonella entericase

PDB DOI: https://doi.org/10.2210/pdb3HYQ/pdb

Classification: ISOMERASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-22 Released: 2009-06-30
Deposition Author(s): Kim, Y., Zhou, M., Peterson, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free:
0.187 (Depositor), 0.186 (DCC)
R-Value Work:
0.163 (Depositor), 0.159 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Isopentenyl-Diphosphate delta-Isomerase from Salmonella entericase

Kim, Y., Zhou, M., Peterson, S., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 21.26 kDa
Atom Count: 1,628
Modeled Residue Count: 151
Deposited Residue Count: 184
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isopentenyl-diphosphate Delta-isomerase	A	184	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: idi EC: 5.3.3.2
UniProt
Find proteins for Q8ZM82 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZM82 Go to UniProtKB: Q8ZM82
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ZM82
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free: 0.187 (Depositor), 0.186 (DCC)
R-Value Work: 0.163 (Depositor), 0.159 (DCC)
R-Value Observed: 0.164 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.443	α = 90
b = 64.152	β = 101.36
c = 35.187	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-06-30

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-06-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.