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- PDB-5buk: Structure of flavin-dependent chlorinase Mpy16 -

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Basic information

Entry
Database: PDB / ID: 5buk
TitleStructure of flavin-dependent chlorinase Mpy16
ComponentsFADH2-dependent halogenase
KeywordsOXIDOREDUCTASE / 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 / FADH2-dependent halogenase
Similarity search - Component
Biological speciesStreptomyces sp. CNQ-418 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 3, 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

Downloads & links

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Assembly

Deposited unit
A: FADH2-dependent halogenase
B: FADH2-dependent halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2595
Polymers100,5962
Non-polymers1,6633
Water7,710428
1
A: FADH2-dependent halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1753
Polymers50,2981
Non-polymers8782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FADH2-dependent halogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0832
Polymers50,2981
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.831, 73.276, 189.717
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FADH2-dependent halogenase


Mass: 50297.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. CNQ-418 (bacteria) / Gene: mpy16 / Production host: Escherichia coli (E. coli) / References: UniProt: J7H1A1
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG4000

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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: Mar 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 64779 / % possible obs: 100 % / Redundancy: 12 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 37.63
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
HKL-2000data collection
PDB_EXTRACT3.15data extraction
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E1T

3e1t


Resolution: 1.95→38.08 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2121 3276 5.06 %
Rwork0.1704 --
obs0.1725 64699 99.85 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.163 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1458 Å20 Å20 Å2
2--0.0376 Å20 Å2
3---0.1082 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6802 0 112 428 7342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077131
X-RAY DIFFRACTIONf_angle_d1.0369689
X-RAY DIFFRACTIONf_dihedral_angle_d14.3592577
X-RAY DIFFRACTIONf_chiral_restr0.0751045
X-RAY DIFFRACTIONf_plane_restr0.0051245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9499-1.9790.26871450.19612570X-RAY DIFFRACTION97
1.979-2.00990.24211320.16952627X-RAY DIFFRACTION100
2.0099-2.04280.2171290.16952654X-RAY DIFFRACTION100
2.0428-2.07810.22381320.16232638X-RAY DIFFRACTION100
2.0781-2.11590.24811360.16972631X-RAY DIFFRACTION100
2.1159-2.15650.22141280.17612673X-RAY DIFFRACTION100
2.1565-2.20060.20361440.17082631X-RAY DIFFRACTION100
2.2006-2.24840.25561530.17052639X-RAY DIFFRACTION100
2.2484-2.30070.24591490.1712628X-RAY DIFFRACTION100
2.3007-2.35820.23471460.17412649X-RAY DIFFRACTION100
2.3582-2.4220.2311220.16952671X-RAY DIFFRACTION100
2.422-2.49320.23921220.1762670X-RAY DIFFRACTION100
2.4932-2.57370.23331460.17722635X-RAY DIFFRACTION100
2.5737-2.66570.24141410.1872664X-RAY DIFFRACTION100
2.6657-2.77240.22561470.1992660X-RAY DIFFRACTION100
2.7724-2.89850.24421500.18982659X-RAY DIFFRACTION100
2.8985-3.05120.2921590.18652675X-RAY DIFFRACTION100
3.0512-3.24230.19711460.18292664X-RAY DIFFRACTION100
3.2423-3.49250.20021620.1682707X-RAY DIFFRACTION100
3.4925-3.84370.17621520.1582688X-RAY DIFFRACTION100
3.8437-4.39920.2021300.14692738X-RAY DIFFRACTION100
4.3992-5.53970.16461330.14622762X-RAY DIFFRACTION100
5.5397-38.08750.18941720.1852890X-RAY DIFFRACTION100

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