4JXU | pdb_00004jxu

Structure of aminotransferase ilvE2 from Sinorhizobium meliloti complexed with PLP

PDB DOI: https://doi.org/10.2210/pdb4JXU/pdb

Classification: TRANSFERASE
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-03-28 Released: 2013-05-29
Deposition Author(s): Cooper, D.R., Cymborowski, M.T., Majorek, K.A., Niedzialkowska, E., Porebski, P.J., Stead, M., Hammonds, J., Seidel, R., Ahmed, M., Bonanno, J.B., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.212 (Depositor), 0.221 (DCC)
R-Value Work:
0.167 (Depositor), 0.178 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of aminotransferase ilvE2 from Sinorhizobium meliloti complexed with PLP

Cooper, D.R., Cymborowski, M.T., A Majorek, K., Niedzialkowska, E., Porebski, P.J., Stead, M., Hammonds, J., Seidel, R., Ahmed, M., Bonanno, J.B., Almo, S.C., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 66.05 kDa
Atom Count: 4,525
Modeled Residue Count: 565
Deposited Residue Count: 590
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative aminotransferase	A, B	295	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: ilvE2, R00971, SMc00042 EC: 2.6.1.42
UniProt
Find proteins for Q92RC2 (Rhizobium meliloti (strain 1021)) Explore Q92RC2 Go to UniProtKB: Q92RC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92RC2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.212 (Depositor), 0.221 (DCC)
R-Value Work: 0.167 (Depositor), 0.178 (DCC)
R-Value Observed: 0.169 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.799	α = 90
b = 76.006	β = 90
c = 93.669	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELXD	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-05-29

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-05-29
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Structure summary
Version 1.3: 2022-04-13
Changes: Database references, Derived calculations, Structure summary