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), 0.224 (DCC)
R-Value Work:
0.174 (Depositor), 0.183 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7EME

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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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

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), 0.224 (DCC)
R-Value Work: 0.174 (Depositor), 0.183 (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

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Ligand Structure Quality Assessment

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.