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- PDB-5bul: Structure of flavin-dependent brominase Bmp2 triple mutant Y302S ... -

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Basic information

Entry
Database: PDB / ID: 5bul
TitleStructure of flavin-dependent brominase Bmp2 triple mutant Y302S F306V A345W
Componentsflavin-dependent halogenase triple mutant
KeywordsHYDROLASE / flavin-dependent enzyme
Function / homology
Function and homology information


FAD binding / oxidoreductase activity
Similarity search - Function
Tryptophan halogenase / : / FAD-binding domain / FAD binding domain / 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
FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent halogenase triple mutant
Similarity search - Component
Biological speciesStreptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9784 Å
AuthorsAgarwal, V. / Louie, G.V. / Noel, J.P. / Moore, B.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Biosynthesis of coral settlement cue tetrabromopyrrole in marine bacteria by a uniquely adapted brominase-thioesterase enzyme pair.
Authors: El Gamal, A. / Agarwal, V. / Diethelm, S. / Rahman, I. / Schorn, M.A. / Sneed, J.M. / Louie, G.V. / Whalen, K.E. / Mincer, T.J. / Noel, J.P. / Paul, V.J. / Moore, B.S.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: flavin-dependent halogenase triple mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8152
Polymers46,0291
Non-polymers7861
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.232, 51.531, 77.062
Angle α, β, γ (deg.)90.00, 100.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein flavin-dependent halogenase triple mutant


Mass: 46029.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140UHM1*PLUS
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.1 Å3/Da / Density % sol: 41.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.978→40 Å / Num. obs: 26147 / % possible obs: 98.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 30.01

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
HKL-2000data collection
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BVA

5bva


Resolution: 1.9784→32.974 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2145 1308 5.01 %
Rwork0.1788 --
obs0.1806 26126 97.98 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.538 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20.1655 Å2
2--0.3533 Å20 Å2
3----0.2333 Å2
Refinement stepCycle: LAST / Resolution: 1.9784→32.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 53 219 3368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073234
X-RAY DIFFRACTIONf_angle_d1.0854382
X-RAY DIFFRACTIONf_dihedral_angle_d14.9781171
X-RAY DIFFRACTIONf_chiral_restr0.074450
X-RAY DIFFRACTIONf_plane_restr0.004561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9784-2.05760.2511280.18272513X-RAY DIFFRACTION90
2.0576-2.15120.23661410.18352733X-RAY DIFFRACTION98
2.1512-2.26460.2221350.16922762X-RAY DIFFRACTION99
2.2646-2.40650.21471530.17362757X-RAY DIFFRACTION99
2.4065-2.59220.271540.17862800X-RAY DIFFRACTION99
2.5922-2.85290.20741340.19122806X-RAY DIFFRACTION100
2.8529-3.26540.21231580.18552792X-RAY DIFFRACTION99
3.2654-4.11280.18481580.1622820X-RAY DIFFRACTION100
4.1128-32.97810.21191470.18672835X-RAY DIFFRACTION98

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