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- PDB-5lv9: Crystal structure of thermophilic tryptophan halogenase (Th-Hal) ... -

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Basic information

Entry
Database: PDB / ID: 5lv9
TitleCrystal structure of thermophilic tryptophan halogenase (Th-Hal) enzyme from Streptomycin violaceusniger.
Componentsthermophilic tryptophan halogenase
KeywordsHYDROLASE / thermophilic / flavin reductase / enzyme
Function / homology
Function and homology information


monooxygenase activity / nucleotide binding
Similarity search - Function
Flavin-dependent tryptophan halogenase / Flavin-dependent halogenase / Tryptophan halogenase / : / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
Thermophilic tryptophan halogenase
Similarity search - Component
Biological speciesStreptomyces violaceusniger (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.33 Å
AuthorsDunstan, M.S. / Menon, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
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 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 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: thermophilic tryptophan halogenase
B: thermophilic tryptophan halogenase


Theoretical massNumber of molelcules
Total (without water)115,9392
Polymers115,9392
Non-polymers00
Water6,792377
1
A: thermophilic tryptophan halogenase


Theoretical massNumber of molelcules
Total (without water)57,9691
Polymers57,9691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: thermophilic tryptophan halogenase


Theoretical massNumber of molelcules
Total (without water)57,9691
Polymers57,9691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.140, 67.140, 477.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein thermophilic tryptophan halogenase


Mass: 57969.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces violaceusniger (bacteria) / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A1L1QK36*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.06 M divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dehydrate) in 0.1 M buffer (1.0M imidazole + MES monohydrate acid buffer) at pH 6.5 made up with a 50% v/v ...Details: 0.06 M divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dehydrate) in 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 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350).

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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: 2.33→57.7 Å / Num. obs: 51611 / % possible obs: 99.7 % / Redundancy: 9.9 % / Net I/σ(I): 11.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.33→56.493 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.2
RfactorNum. reflection% reflection
Rfree0.2243 2546 4.95 %
Rwork0.1789 --
obs0.1812 51445 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.17 Å2 / Biso mean: 43.1279 Å2 / Biso min: 17.19 Å2
Refinement stepCycle: final / Resolution: 2.33→56.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8133 0 0 377 8510
Biso mean---42.39 -
Num. residues----1022
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.01811.2499-0.41461.6291-0.70121.4389-0.0106-0.2051-0.0238-0.0952-0.12330.06560.0961-0.2462-0.00730.4245-0.0694-0.01090.2619-0.00210.232942.65436.0627206.1986
20.03730.22190.02140.4004-0.37191.52770.15210.11670.0730.1173-0.040.1192-0.0704-0.2364-0.0060.463-0.1354-0.00050.1598-0.01050.30442.7421-1.8297215.506
30.2843-0.0257-0.14160.569-0.10941.6590.03920.046-0.040.0174-0.03920.05580.2807-0.04210.00510.439-0.0925-0.05010.1415-0.00210.24848.0973-11.0417219.145
41.0965-0.7765-0.00981.6801-1.17251.9240.0604-0.08290.17420.1551-0.156-0.1350.0406-0.1847-0.00280.3311-0.1186-0.01110.22210.03380.257746.47872.1855261.783
50.27350.1036-0.29511.15070.05641.24620.0173-0.05430.0252-0.15350.05540.1928-0.0167-0.2395-0.03250.3231-0.0946-0.06160.17910.02360.270144.860212.4766250.3569
60.22630.15160.04030.9207-0.01621.5391-0.0186-0.07720.0202-0.14790.01460.0978-0.1775-0.01090.01310.3113-0.0955-0.02040.1736-0.01670.244554.333118.8259246.3214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 72 )A2 - 72
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 244 )A73 - 244
3X-RAY DIFFRACTION3chain 'A' and (resid 245 through 510 )A245 - 510
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 49 )B2 - 49
5X-RAY DIFFRACTION5chain 'B' and (resid 50 through 244 )B50 - 244
6X-RAY DIFFRACTION6chain 'B' and (resid 245 through 514 )B245 - 514

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