3TXV | pdb_00003txv

Crystal structure of a probable tagatose 6 phosphate kinase from Sinorhizobium meliloti 1021

PDB DOI: https://doi.org/10.2210/pdb3TXV/pdb

Classification: TRANSFERASE
Organism(s): Sinorhizobium meliloti
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-09-23 Released: 2011-10-12
Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., LaFleur, J., Seidel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.293 (Depositor), 0.294 (DCC)
R-Value Work:
0.240 (Depositor), 0.243 (DCC)
R-Value Observed:
0.243 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a probable tagatose 6 phosphate kinase from Sinorhizobium meliloti 1021

Agarwal, R., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 49.42 kDa
Atom Count: 2,878
Modeled Residue Count: 387
Deposited Residue Count: 450
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable tagatose 6-phosphate kinase	A	450	Sinorhizobium meliloti	Mutation(s): 0 Gene Names: RB0951, SM_b21373 EC: 2.7.1.144
UniProt
Find proteins for Q92UY3 (Rhizobium meliloti (strain 1021)) Explore Q92UY3 Go to UniProtKB: Q92UY3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92UY3
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: 2.80 Å
R-Value Free: 0.293 (Depositor), 0.294 (DCC)
R-Value Work: 0.240 (Depositor), 0.243 (DCC)
R-Value Observed: 0.243 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.005	α = 90
b = 140.005	β = 90
c = 97.356	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
PHASER	phasing
CCP4	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-10-12

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2011-10-12
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 2024-11-06
Changes: Structure summary