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- PDB-6oyu: Structure of an ancestral-reconstructed cytochrome P450 1B1 with ... -

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Basic information

Entry
Database: PDB / ID: 6oyu
TitleStructure of an ancestral-reconstructed cytochrome P450 1B1 with alpha-naphthoflavone
ComponentsCytochrome P450 1B1
KeywordsOXIDOREDUCTASE / CYP1B1 / ancestral reconstruction / mammalian
Function / homologyCytochrome p450 / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha / 2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsBart, A.G. / Harris, K.L. / Scott, E.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM076343 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure of an ancestral mammalian family 1B1 cytochrome P450 with increased thermostability.
Authors: Bart, A.G. / Harris, K.L. / Gillam, E.M.J. / Scott, E.E.
History
DepositionMay 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 6, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 13, 2020Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Oct 11, 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: Cytochrome P450 1B1
B: Cytochrome P450 1B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,66418
Polymers110,7002
Non-polymers3,96416
Water79344
1
A: Cytochrome P450 1B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2408
Polymers55,3501
Non-polymers1,8907
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 1B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,42410
Polymers55,3501
Non-polymers2,0749
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)164.641, 164.641, 96.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Cytochrome P450 1B1


Mass: 55349.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-BHF / 2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE / 7,8-BENZOFLAVONE / ALPHA-NAPHTHOFLAVONE


Mass: 272.297 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C19H12O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 900 mM sodium citrate tribasic, 90 mM Tris base / HCl pH 7.0, 180 mM NaCl, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 27530 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.998 / Rpim(I) all: 0.064 / Net I/σ(I): 53
Reflection shellResolution: 2.95→3 Å / Mean I/σ(I) obs: 5 / Num. unique obs: 1364 / CC1/2: 0.399 / Rpim(I) all: 0.788

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PM0

3pm0


Resolution: 2.95→48.15 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.1
RfactorNum. reflection% reflection
Rfree0.2577 1983 7.62 %
Rwork0.1992 --
obs0.2037 26007 95.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.95→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7330 0 204 44 7578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067760
X-RAY DIFFRACTIONf_angle_d0.67910557
X-RAY DIFFRACTIONf_dihedral_angle_d21.5852806
X-RAY DIFFRACTIONf_chiral_restr0.0421091
X-RAY DIFFRACTIONf_plane_restr0.0031360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9504-3.02420.38740.2681942X-RAY DIFFRACTION53
3.0242-3.10590.33041290.26671540X-RAY DIFFRACTION86
3.1059-3.19730.34871450.25061764X-RAY DIFFRACTION99
3.1973-3.30050.28851520.23191782X-RAY DIFFRACTION100
3.3005-3.41840.31821420.23171769X-RAY DIFFRACTION100
3.4184-3.55520.2881480.21311795X-RAY DIFFRACTION100
3.5552-3.7170.27361530.1971808X-RAY DIFFRACTION100
3.717-3.91280.30381450.18621776X-RAY DIFFRACTION100
3.9128-4.15790.23381460.1911785X-RAY DIFFRACTION100
4.1579-4.47870.22441490.17291796X-RAY DIFFRACTION100
4.4787-4.9290.22281510.16951790X-RAY DIFFRACTION100
4.929-5.64130.25011480.20051817X-RAY DIFFRACTION100
5.6413-7.10380.25851530.21671806X-RAY DIFFRACTION100
7.1038-48.15690.20221480.17671854X-RAY DIFFRACTION99

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