1TK9 | pdb_00001tk9

Crystal Structure of Phosphoheptose isomerase 1

PDB DOI: https://doi.org/10.2210/pdb1TK9/pdb

Classification: ISOMERASE
Organism(s): Campylobacter jejuni
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-06-08 Released: 2004-06-22
Deposition Author(s): Rajashankar, K.R., Solorzano, V., Kniewel, R., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.211 (Depositor), 0.220 (DCC)
R-Value Work:
0.182 (Depositor), 0.194 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history.

Literature

Crystal structures of two putative phosphoheptose isomerases.

Seetharaman, J., Rajashankar, K.R., Solorzano, V., Kniewel, R., Lima, C.D., Bonanno, J.B., Burley, S.K., Swaminathan, S.

(2006) Proteins 63: 1092-1096

PubMed: 16477602 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/prot.20908
Primary Citation Related Structures:
1TK9, 1X94

Organizational Affiliation

Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA.

Macromolecule Content

Total Structure Weight: 82.18 kDa
Atom Count: 6,367
Modeled Residue Count: 752
Deposited Residue Count: 752
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoheptose isomerase 1	A, B, C, D	188	Campylobacter jejuni	Mutation(s): 4 Gene Names: LPCA1, GMHA1, CJ1149C EC: 5 (PDB Primary Data), 5.3.1.28 (UniProt)
UniProt
Find proteins for Q9PNE6 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PNE6 Go to UniProtKB: Q9PNE6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9PNE6
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.211 (Depositor), 0.220 (DCC)
R-Value Work: 0.182 (Depositor), 0.194 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.657	α = 90
b = 123.289	β = 90
c = 127.804	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-06-22

Deposition Author(s):

Rajashankar, K.R.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2004-06-22
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-04-03
Changes: Data collection, Database references, Refinement description
Version 1.5: 2024-10-30
Changes: 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.