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- PDB-5lva: Crystal structure of thermophilic tryptophan halogenase (Th-Hal) ... -

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Basic information

Entry
Database: PDB / ID: 5lva
TitleCrystal structure of thermophilic tryptophan halogenase (Th-Hal) enzyme from Streptomycin violaceusniger.
ComponentsNAD(P)H-FMN oxidoreductase
KeywordsOXIDOREDUCTASE / thermophilic / flavin reductase / enzyme
Function / homology
Function and homology information


NAD(P)H dehydrogenase (quinone) activity / FMN binding / electron transfer activity
Similarity search - Function
: / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NAD(P)H-FMN oxidoreductase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.53 Å
AuthorsDunstan, M.S. / Menon, B.
CitationJournal: Org.Biomol.Chem. / Year: 2016
Title: Structure and biocatalytic scope of thermophilic flavin-dependent halogenase and flavin reductase enzymes.
Authors: Menon, B.R. / Latham, J. / Dunstan, M.S. / Brandenburger, E. / Klemstein, U. / Leys, D. / Karthikeyan, C. / Greaney, M.F. / Shepherd, S.A. / Micklefield, J.
History
DepositionSep 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD(P)H-FMN oxidoreductase
B: NAD(P)H-FMN oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2794
Polymers39,3662
Non-polymers9132
Water2,486138
1
A: NAD(P)H-FMN oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1402
Polymers19,6831
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD(P)H-FMN oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1402
Polymers19,6831
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.840, 66.840, 335.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein NAD(P)H-FMN oxidoreductase


Mass: 19683.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: frb / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q75V96
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M amino acids in a 0.1 M buffer (1.0M imidazole + MES monohydrate acid buffer) at pH 6.5 made up with a 50% v/v precipitant mix (that contained 10% w/v PEG 20,000; 20% v/v PEG MME 550)

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.53→54.71 Å / Num. obs: 15952 / % possible obs: 99.9 % / Redundancy: 18.4 % / Net I/σ(I): 19.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
RefinementResolution: 2.53→51.391 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.35
RfactorNum. reflection% reflection
Rfree0.2383 777 4.9 %
Rwork0.183 --
obs0.1856 15853 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.71 Å2 / Biso mean: 28.1904 Å2 / Biso min: 11.03 Å2
Refinement stepCycle: final / Resolution: 2.53→51.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 62 138 2967
Biso mean--22.53 29.61 -
Num. residues----346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092930
X-RAY DIFFRACTIONf_angle_d1.1853998
X-RAY DIFFRACTIONf_chiral_restr0.051417
X-RAY DIFFRACTIONf_plane_restr0.006507
X-RAY DIFFRACTIONf_dihedral_angle_d14.8141036
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.53-2.68860.29111210.214824332554
2.6886-2.89610.29531300.220824332563
2.8961-3.18750.30331290.222824392568
3.1875-3.64870.27431380.199124702608
3.6487-4.59650.19161290.154325352664
4.5965-51.40140.19181300.160827662896

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