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- PDB-7cp6: Crystal structure of FqzB -

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Basic information

Entry
Database: PDB / ID: 7cp6
TitleCrystal structure of FqzB
ComponentsMAK1-like monooxygenase
KeywordsOXIDOREDUCTASE / flavin adenine dinucleotide / FAD-dependent monooxygenase
Function / homology
Function and homology information


secondary metabolite biosynthetic process / FAD binding / monooxygenase activity
Similarity search - Function
FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / IODIDE ION / MAK1-like monooxygenase
Similarity search - Component
Biological speciesAspergillus fumigatus Z5 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAK1-like monooxygenase
B: MAK1-like monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,86914
Polymers101,9552
Non-polymers2,91412
Water3,369187
1
A: MAK1-like monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3446
Polymers50,9781
Non-polymers1,3675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-24 kcal/mol
Surface area18960 Å2
MethodPISA
2
B: MAK1-like monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5258
Polymers50,9781
Non-polymers1,5477
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-5 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.893, 120.181, 68.048
Angle α, β, γ (deg.)90.000, 94.111, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein MAK1-like monooxygenase


Mass: 50977.641 Da / Num. of mol.: 2 / 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.: 2 / 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.: 9 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#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
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, 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: 1.00563 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: 1.00563 Å / Relative weight: 1
ReflectionResolution: 2.2→41.64 Å / Num. obs: 45285 / % possible obs: 99.7 % / Redundancy: 13.6 % / Biso Wilson estimate: 35.71 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.124 / Net I/σ(I): 14.87
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.822 / Num. unique obs: 4430 / CC1/2: 0.837

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.2→41.64 Å / SU ML: 0.2697 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 25.7452
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2377 2257 4.99 %
Rwork0.2126 43013 -
obs0.2139 45270 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6577 0 116 187 6880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816854
X-RAY DIFFRACTIONf_angle_d0.69049339
X-RAY DIFFRACTIONf_chiral_restr0.04651023
X-RAY DIFFRACTIONf_plane_restr0.0031186
X-RAY DIFFRACTIONf_dihedral_angle_d12.42112435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.27351310.22592622X-RAY DIFFRACTION96.33
2.25-2.30.27681490.23882656X-RAY DIFFRACTION99.96
2.3-2.360.30691570.23992669X-RAY DIFFRACTION100
2.36-2.420.30721420.25752716X-RAY DIFFRACTION100
2.42-2.490.30451420.25472643X-RAY DIFFRACTION100
2.49-2.570.29921320.25612701X-RAY DIFFRACTION100
2.57-2.670.3121290.25992711X-RAY DIFFRACTION100
2.67-2.770.28221440.24492667X-RAY DIFFRACTION99.96
2.77-2.90.27691490.25172675X-RAY DIFFRACTION100
2.9-3.050.28811300.242708X-RAY DIFFRACTION100
3.05-3.240.24161250.23192724X-RAY DIFFRACTION100
3.24-3.490.24981450.21012698X-RAY DIFFRACTION100
3.49-3.850.19321380.19762684X-RAY DIFFRACTION100
3.85-4.40.19741370.17422698X-RAY DIFFRACTION100
4.4-5.540.20281370.17982725X-RAY DIFFRACTION100
5.54-41.640.2031700.19282716X-RAY DIFFRACTION99.72

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