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- PDB-7qan: Cytochrome P450 Enzyme AbyV -

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Basic information

Entry
Database: PDB / ID: 7qan
TitleCytochrome P450 Enzyme AbyV
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Micromonospora maris / abyssomicin / heme / monooxygenase
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cytochrome P450
Similarity search - Component
Biological speciesMicromonospora maris
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsParnell, A.E. / Back, C.R. / Race, P.R.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L01386X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M025624/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M012107/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T001968/1 United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: The Role of Cytochrome P450 AbyV in the Final Stages of Abyssomicin C Biosynthesis.
Authors: Devine, A.J. / Parnell, A.E. / Back, C.R. / Lees, N.R. / Johns, S.T. / Zulkepli, A.Z. / Barringer, R. / Zorn, K. / Stach, J.E.M. / Crump, M.P. / Hayes, M.A. / van der Kamp, M.W. / Race, P.R. / Willis, C.L.
History
DepositionNov 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 18, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Cytochrome P450
BBB: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,10923
Polymers88,7792
Non-polymers3,33021
Water2,612145
1
AAA: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,96218
Polymers44,3891
Non-polymers2,57317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1475
Polymers44,3891
Non-polymers7574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.770, 91.830, 82.550
Angle α, β, γ (deg.)90.000, 92.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Cytochrome P450


Mass: 44389.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora maris (strain DSM 45365 / JCM 31040 / NBRC 109089 / NRRL B-24793 / AB-18-032) (bacteria)
Strain: DSM 45365 / JCM 31040 / NBRC 109089 / NRRL B-24793 / AB-18-032
Gene: abyV, VAB18032_16385 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4F6Q5

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Non-polymers , 9 types, 166 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris pH 7, 25% PEG3350, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.01→61.438 Å / Num. obs: 50350 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.092 / Net I/σ(I): 14
Reflection shellResolution: 2.01→2.06 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3703 / CC1/2: 0.728 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ABB

3abb


Resolution: 2.01→61.438 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.177 / Average fsc free: 0.8347 / Average fsc work: 0.8499 / Cross valid method: FREE R-VALUE / ESU R: 0.188 / ESU R Free: 0.169
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2383 2409 4.787 %
Rwork0.1903 47920 -
all0.193 --
obs-50329 99.814 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.391 Å2
Baniso -1Baniso -2Baniso -3
1--2.387 Å20 Å20.635 Å2
2---3.326 Å20 Å2
3---5.641 Å2
Refinement stepCycle: LAST / Resolution: 2.01→61.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5410 0 221 145 5776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135730
X-RAY DIFFRACTIONr_bond_other_d0.0350.0175494
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.6857795
X-RAY DIFFRACTIONr_angle_other_deg2.3261.60612608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.495719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.74219.623292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.715828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.221561
X-RAY DIFFRACTIONr_chiral_restr0.0820.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026432
X-RAY DIFFRACTIONr_gen_planes_other0.0150.021247
X-RAY DIFFRACTIONr_nbd_refined0.2050.21255
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.25150
X-RAY DIFFRACTIONr_nbtor_refined0.1540.22740
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.22574
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2164
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0020.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.218
X-RAY DIFFRACTIONr_nbd_other0.2090.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.130.215
X-RAY DIFFRACTIONr_mcbond_it3.7855.3322891
X-RAY DIFFRACTIONr_mcbond_other3.7865.3312890
X-RAY DIFFRACTIONr_mcangle_it5.4597.9773605
X-RAY DIFFRACTIONr_mcangle_other5.4587.9773606
X-RAY DIFFRACTIONr_scbond_it3.9745.7492839
X-RAY DIFFRACTIONr_scbond_other3.9745.7512840
X-RAY DIFFRACTIONr_scangle_it5.9768.4154190
X-RAY DIFFRACTIONr_scangle_other5.9768.4164191
X-RAY DIFFRACTIONr_lrange_it8.23563.6066179
X-RAY DIFFRACTIONr_lrange_other8.2363.6116172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.0620.3451710.3323520X-RAY DIFFRACTION99.8647
2.062-2.1190.3041730.2983437X-RAY DIFFRACTION99.5313
2.119-2.180.2861640.2683338X-RAY DIFFRACTION99.9144
2.18-2.2470.2891630.2583288X-RAY DIFFRACTION99.9131
2.247-2.3210.3111700.2543120X-RAY DIFFRACTION99.6668
2.321-2.4020.2351600.2113025X-RAY DIFFRACTION99.9372
2.402-2.4930.2521600.2032945X-RAY DIFFRACTION99.9356
2.493-2.5940.261480.1952811X-RAY DIFFRACTION99.9662
2.594-2.710.2751450.1782709X-RAY DIFFRACTION99.86
2.71-2.8420.2431280.1882635X-RAY DIFFRACTION100
2.842-2.9950.2491120.192489X-RAY DIFFRACTION99.9232
2.995-3.1770.251100.1852385X-RAY DIFFRACTION99.9599
3.177-3.3960.2491050.1772186X-RAY DIFFRACTION99.8692
3.396-3.6680.249840.1792063X-RAY DIFFRACTION99.814
3.668-4.0170.236980.1631870X-RAY DIFFRACTION99.7466
4.017-4.490.164980.1441706X-RAY DIFFRACTION99.834
4.49-5.1830.205730.1491536X-RAY DIFFRACTION99.9379
5.183-6.3420.222580.1951300X-RAY DIFFRACTION100
6.342-8.9480.289550.189986X-RAY DIFFRACTION99.8082
8.948-61.4380.161340.169571X-RAY DIFFRACTION99.835

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