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- PDB-7cp7: Crystal structure of FqzB, native proteins -

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Basic information

Entry
Database: PDB / ID: 7cp7
TitleCrystal structure of FqzB, native proteins
ComponentsMAK1-like monooxygenase
KeywordsOXIDOREDUCTASE / monooxygenase (FAD)
Function / homologyFAD-binding domain / FAD binding domain / secondary metabolite biosynthetic process / FAD binding / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / IODIDE ION / MAK1-like monooxygenase
Function and homology information
Biological speciesAspergillus fumigatus Z5 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHara, K. / Hashimoto, H. / Matsushita, T. / Kishimoto, S. / Watanabe, K.
CitationJournal: Biochemistry / Year: 2020
Title: Structural and Functional Analyses of a Spiro-Carbon-Forming, Highly Promiscuous Epoxidase from Fungal Natural Product Biosynthesis.
Authors: Matsushita, T. / Kishimoto, S. / Hara, K. / Hashimoto, H. / Watanabe, K.
History
DepositionAug 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: MAK1-like monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5258
Polymers50,9781
Non-polymers1,5477
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-5 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.563, 68.350, 121.895
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein MAK1-like monooxygenase


Mass: 50977.641 Da / Num. of mol.: 1 / Mutation: L119I,A140T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Z5 (mold) / Gene: Y699_04337 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J5T0B0
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Bis-Tris propane, sodium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.39→19.66 Å / Num. obs: 18774 / % possible obs: 99.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 38.86 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.122 / Net I/σ(I): 11.78
Reflection shellResolution: 2.39→2.48 Å / Rmerge(I) obs: 0.698 / Num. unique obs: 1794 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CP6

7cp6


Resolution: 2.4→19.66 Å / SU ML: 0.3346 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.7918
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2704 955 5.09 %
Rwork0.2213 17812 -
obs0.2239 18767 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.71 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3353 0 59 63 3475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773495
X-RAY DIFFRACTIONf_angle_d0.7714761
X-RAY DIFFRACTIONf_chiral_restr0.0451518
X-RAY DIFFRACTIONf_plane_restr0.0032605
X-RAY DIFFRACTIONf_dihedral_angle_d14.92981238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.520.37041140.2732491X-RAY DIFFRACTION97.97
2.52-2.680.32281350.26072498X-RAY DIFFRACTION99.96
2.68-2.890.31491330.2672498X-RAY DIFFRACTION99.89
2.89-3.180.34611230.25952537X-RAY DIFFRACTION99.92
3.18-3.630.31350.22542545X-RAY DIFFRACTION99.89
3.63-4.570.21451440.18642575X-RAY DIFFRACTION99.89
4.57-19.660.24061710.20012668X-RAY DIFFRACTION100

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