4MYM | pdb_00004mym

Crystal structure of a glyoxalase/ bleomycin resistance protein/ dioxygenase from Nocardioides

PDB DOI: https://doi.org/10.2210/pdb4MYM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Nocardioides sp. JS614
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2013-09-27 Released: 2013-12-25
Deposition Author(s): Eswaramoorthy, S., Chamala, S., Evans, B., Foti, F., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., AL Obaidi, N., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.217 (Depositor), 0.216 (DCC)
R-Value Work:
0.186 (Depositor), 0.195 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a glyoxalase/ bleomycin resistance protein/ dioxygenase from Nocardioides.

Eswaramoorthy, S., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 19.98 kDa
Atom Count: 1,249
Modeled Residue Count: 151
Deposited Residue Count: 176
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resistance protein/dioxygenase	A	176	Nocardioides sp. JS614	Mutation(s): 0 Gene Names: Noca_4190
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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: 1.90 Å
R-Value Free: 0.217 (Depositor), 0.216 (DCC)
R-Value Work: 0.186 (Depositor), 0.195 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.66	α = 90
b = 83.589	β = 90
c = 102.413	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-12-25

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-12-25
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary