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

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Basic information

Entry
Database: PDB / ID: 6oyv
TitleStructure of an ancestral-reconstructed cytochrome P450 1B1 with estradiol
ComponentsCytochrome P450 1B1
KeywordsOXIDOREDUCTASE / CYP1B1 / ancestral reconstruction / mammalian
Function / homologyCytochrome p450 / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha / ESTRADIOL / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.101 Å
AuthorsBart, A.G. / 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)112,4786
Polymers110,7002
Non-polymers1,7784
Water0
1
A: Cytochrome P450 1B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2393
Polymers55,3501
Non-polymers8892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 1B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2393
Polymers55,3501
Non-polymers8892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)162.362, 162.362, 95.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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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-EST / ESTRADIOL / Estradiol


Mass: 272.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 M sodium citrate tribasic, 0.1 M tris/HCl pH 7.0, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→38.27 Å / Num. obs: 22678 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 106.18 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.047 / Net I/σ(I): 10.4
Reflection shellResolution: 3.1→3.31 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4085 / CC1/2: 0.688 / Rpim(I) all: 0.883 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472)refinement
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OYU

6oyu


Resolution: 3.101→38.269 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.49
RfactorNum. reflection% reflection
Rfree0.2765 2001 9.02 %
Rwork0.2434 --
obs0.2464 22189 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.101→38.269 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7245 0 40 0 7285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037498
X-RAY DIFFRACTIONf_angle_d0.60910208
X-RAY DIFFRACTIONf_dihedral_angle_d21.6942735
X-RAY DIFFRACTIONf_chiral_restr0.041089
X-RAY DIFFRACTIONf_plane_restr0.0051318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1005-3.1780.37621110.36761122X-RAY DIFFRACTION76
3.178-3.26390.40781360.34441382X-RAY DIFFRACTION95
3.2639-3.35990.3531450.33751474X-RAY DIFFRACTION100
3.3599-3.46830.38541440.32931462X-RAY DIFFRACTION100
3.4683-3.59210.3121430.31251459X-RAY DIFFRACTION100
3.5921-3.73580.3481460.30341457X-RAY DIFFRACTION100
3.7358-3.90570.32381440.29121471X-RAY DIFFRACTION100
3.9057-4.11140.33421440.28041451X-RAY DIFFRACTION100
4.1114-4.36860.29641480.2681482X-RAY DIFFRACTION100
4.3686-4.70540.23651440.2321468X-RAY DIFFRACTION100
4.7054-5.17790.25251450.23431471X-RAY DIFFRACTION100
5.1779-5.92480.28071510.24781493X-RAY DIFFRACTION100
5.9248-7.45550.30161470.24891467X-RAY DIFFRACTION100
7.4555-38.2720.20941530.16841529X-RAY DIFFRACTION100

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