3DR5 | pdb_00003dr5

Crystal structure of the Q8NRD3_CORGL protein from Corynebacterium glutamicum. Northeast Structural Genomics Consortium target CgR117.

PDB DOI: https://doi.org/10.2210/pdb3DR5/pdb

Classification: structural genomics, unknown function
Organism(s): Corynebacterium glutamicum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-10 Released: 2008-09-09
Deposition Author(s): Vorobiev, S.M., Su, M., Seetharaman, J., Wang, D., Ciccosanti, C., Foote, E.L., Mao, L., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.231 (Depositor), 0.238 (DCC)
R-Value Work:
0.211 (Depositor), 0.216 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the Q8NRD3_CORGL protein from Corynebacterium glutamicum.

Vorobiev, S.M., Su, M., Seetharaman, J., Wang, D., Ciccosanti, C., Foote, E.L., Mao, L., Xiao, R., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 24.01 kDa
Atom Count: 1,781
Modeled Residue Count: 216
Deposited Residue Count: 221
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative O-Methyltransferase	A	221	Corynebacterium glutamicum	Mutation(s): 0 Gene Names: Cgl1119, cg1270
UniProt
Find proteins for Q8NRD3 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NRD3 Go to UniProtKB: Q8NRD3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NRD3
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: 2.25 Å
R-Value Free: 0.231 (Depositor), 0.238 (DCC)
R-Value Work: 0.211 (Depositor), 0.216 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.511	α = 90
b = 50.511	β = 90
c = 303.33	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXDE	phasing
RESOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-09-09

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-09-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary