7EME | pdb_00007eme

Putative Leptospira interrogans recombinant L-amino acid oxidase

PDB DOI: https://doi.org/10.2210/pdb7EME/pdb

Classification: OXIDOREDUCTASE
Organism(s): Leptospira interrogans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-04-13 Released: 2021-08-18
Deposition Author(s): Vaigundan, D., Yuvaraj, I., Krishnaswamy, P.R., Sekar, K., Murthy, M.R.N., Sunita, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.174 (Depositor), 0.180 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural characterization of a putative recombinant L-amino acid oxidase from Leptospira interrogans

Vaigundan, D., Yuvaraj, I., Sunita, P., Sekar, K., Murthy, M.R.N., Krishnaswamy, P.R.

(2022) Curr Sci 123: 895-906

DOI: https://doi.org/10.18520/cs/v123/i7/895-906

Macromolecule Content

Total Structure Weight: 100.09 kDa
Atom Count: 7,122
Modeled Residue Count: 825
Deposited Residue Count: 894
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)/FAD-dependent oxidoreductase	A, B	447	Leptospira interrogans	Mutation(s): 0 Gene Names: E4414_19605
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
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.174 (Depositor), 0.180 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.756	α = 90
b = 106.229	β = 90
c = 139.916	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-08-18

Deposition Author(s):

Krishnaswamy, P.R.

Revision History (Full details and data files)

Version 1.0: 2021-08-18
Type: Initial release
Version 1.1: 2023-03-01
Changes: Database references
Version 1.2: 2024-05-29
Changes: Data collection

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.