3C3J | pdb_00003c3j

Crystal structure of tagatose-6-phosphate ketose/aldose isomerase from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb3C3J/pdb

Classification: ISOMERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2008-01-28 Released: 2008-02-19
Deposition Author(s): Zhang, R., Skarina, T., Egorova, O., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.185 (Depositor), 0.194 (DCC)
R-Value Work:
0.136 (Depositor), 0.146 (DCC)
R-Value Observed:
0.138 (Depositor)

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

Literature

The crystal structure of the tagatose-6-phosphate ketose/aldose isomerase from Escherichia coli.

Zhang, R., Skarina, T., Egorova, O., Savchenko, A., Edwards, A.M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 253.72 kDa
Atom Count: 19,285
Modeled Residue Count: 2,213
Deposited Residue Count: 2,304
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative tagatose-6-phosphate ketose/aldose isomerase	A, B, C, D, E A, B, C, D, E, F	384	Escherichia coli K-12	Mutation(s): 0 Gene Names: agaS, yraB, b3136, JW3105 EC: 3.5.99
UniProt
Find proteins for P42907 (Escherichia coli (strain K12)) Explore P42907 Go to UniProtKB: P42907
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42907
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, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.185 (Depositor), 0.194 (DCC)
R-Value Work: 0.136 (Depositor), 0.146 (DCC)
R-Value Observed: 0.138 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.941	α = 90
b = 81.211	β = 90.21
c = 138.325	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-02-19

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-02-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2024-10-30
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.