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- PDB-8gu0: Crystal structure of a fungal halogenase RadH -

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Basic information

Entry
Database: PDB / ID: 8gu0
TitleCrystal structure of a fungal halogenase RadH
ComponentsNon-heme halogenase radH
KeywordsFLAVOPROTEIN / Flavin-dependent halogenase enzyme
Function / homology
Function and homology information


flavin-dependent halogenase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / secondary metabolite biosynthetic process / monooxygenase activity
Similarity search - Function
Flavin-dependent halogenase / Tryptophan halogenase / : / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent halogenase radH
Similarity search - Component
Biological speciesFloropilus chiversii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsJiang, S.M. / Brown, C.J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: Biomolecules / Year: 2023
Title: Further Characterization of Fungal Halogenase RadH and Its Homologs.
Authors: Peh, G. / Gunawan, G.A. / Tay, T. / Tiong, E. / Tan, L.L. / Jiang, S. / Goh, Y.L. / Ye, S. / Wong, J. / Brown, C.J. / Zhao, H. / Ang, E.L. / Wong, F.T. / Lim, Y.H.
History
DepositionSep 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-heme halogenase radH
B: Non-heme halogenase radH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,01212
Polymers113,0462
Non-polymers2,96610
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint3 kcal/mol
Surface area35270 Å2
Unit cell
Length a, b, c (Å)135.174, 135.174, 52.693
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 258 or resid 267...
21(chain B and (resid 2 through 258 or resid 267...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERALAALA(chain A and (resid 2 through 258 or resid 267...AA2 - 2582 - 258
12VALVALARGARG(chain A and (resid 2 through 258 or resid 267...AA267 - 519267 - 519
13FADFADFADFAD(chain A and (resid 2 through 258 or resid 267...AC601
14PG4PG4PG4PG4(chain A and (resid 2 through 258 or resid 267...AD602
15PG4PG4PG4PG4(chain A and (resid 2 through 258 or resid 267...AE603
16PG4PG4PG4PG4(chain A and (resid 2 through 258 or resid 267...AF604
17PG4PG4PG4PG4(chain A and (resid 2 through 258 or resid 267...AG605
21SERSERALAALA(chain B and (resid 2 through 258 or resid 267...BB2 - 2582 - 258
22VALVALLEULEU(chain B and (resid 2 through 258 or resid 267...BB267 - 440267 - 440
23FADFADFADFAD(chain B and (resid 2 through 258 or resid 267...BH601
24PG4PG4PG4PG4(chain B and (resid 2 through 258 or resid 267...BI602
25PG4PG4PG4PG4(chain B and (resid 2 through 258 or resid 267...BJ603
26PG4PG4PG4PG4(chain B and (resid 2 through 258 or resid 267...BK604

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Components

#1: Protein Non-heme halogenase radH / Radicicol biosynthesis cluster protein radH


Mass: 56522.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Floropilus chiversii (fungus) / Gene: radH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: C5H881, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one ...References: UniProt: C5H881, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES, pH6.5, 40% PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.42→49.1 Å / Num. obs: 22240 / % possible obs: 91.3 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 11.1
Reflection shellResolution: 2.42→2.6 Å / Num. unique obs: 1112 / CC1/2: 0.483

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Processing

Software
NameVersionClassification
PHENIXdev_3885refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E1T

3e1t


Resolution: 2.42→49.09 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2769 1197 5.39 %
Rwork0.2285 21021 -
obs0.2312 22218 60.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.17 Å2 / Biso mean: 67.1594 Å2 / Biso min: 18.47 Å2
Refinement stepCycle: final / Resolution: 2.42→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6933 0 198 187 7318
Biso mean--66.72 61.31 -
Num. residues----898
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4012X-RAY DIFFRACTION11.13TORSIONAL
12B4012X-RAY DIFFRACTION11.13TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.42-2.520.4362260.354642144711
2.52-2.630.3533570.319392798424
2.64-2.770.3839830.30691411149437
2.77-2.950.33951170.28991772188947
2.95-3.170.38881120.29122191230357
3.18-3.490.30721540.25632785293972
3.5-40.30732040.22383679388395
4-5.040.24472190.197738664085100
5.04-49.090.24912250.22453969419499

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