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- PDB-6c93: Effects of the E310A Mutation of Cytochrome P450 4B1 (CYP4B1) on ... -

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Basic information

Entry
Database: PDB / ID: 6c93
TitleEffects of the E310A Mutation of Cytochrome P450 4B1 (CYP4B1) on n-Octane binding and Heme Ruffling
ComponentsCytochrome P450 4B1
KeywordsOXIDOREDUCTASE / cytochrome P450 / fatty acid omega-hydroxylase / cyp4b1 / n-octane
Function / homology
Function and homology information


unspecific monooxygenase / aromatase activity / iron ion binding / heme binding / endoplasmic reticulum membrane
Similarity search - Function
: / Cytochrome P450, E-class, group I / 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 / N-OCTANE / Cytochrome P450 4B1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.674 Å
AuthorsHsu, M.-H. / Johnson, E.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM031001 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Noncovalent interactions dominate dynamic heme distortion in cytochrome P450 4B1.
Authors: Jennings, G.K. / Hsu, M.H. / Shock, L.S. / Johnson, E.F. / Hackett, J.C.
History
DepositionJan 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 4B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5203
Polymers57,7891
Non-polymers7312
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-15 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.435, 109.435, 126.443
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cytochrome P450 4B1 / CYPIVB1 / Cytochrome P450 isozyme 5


Mass: 57789.344 Da / Num. of mol.: 1 / Mutation: E310A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CYP4B1 / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / Strain (production host): dH5alpha / References: UniProt: P15128, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.78 Å3/Da / Density % sol: 67.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, tri-sodium citrate, sodium chloride, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.674→38.51 Å / Num. obs: 24818 / % possible obs: 98.3 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.8
Reflection shellResolution: 2.674→2.8 Å / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3162 / CC1/2: 0.882 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T6Q

5t6q


Resolution: 2.674→38.51 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / Phase error: 26.47
Details: DivCon 6 Phenix Plug-In used for heme stereo-chemical restraints during refinement
RfactorNum. reflection% reflection
Rfree0.2378 1221 4.93 %
Rwork0.1894 --
obs0.1918 24776 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.674→38.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3894 0 51 6 3951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134067
X-RAY DIFFRACTIONf_angle_d1.0555523
X-RAY DIFFRACTIONf_dihedral_angle_d10.2162389
X-RAY DIFFRACTIONf_chiral_restr0.052573
X-RAY DIFFRACTIONf_plane_restr0.008705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6741-2.78120.29551310.26332478X-RAY DIFFRACTION94
2.7812-2.90770.28121470.23382583X-RAY DIFFRACTION100
2.9077-3.06090.33331290.26092627X-RAY DIFFRACTION99
3.0609-3.25260.3281140.25032598X-RAY DIFFRACTION97
3.2526-3.50360.29711400.23582647X-RAY DIFFRACTION100
3.5036-3.85590.2641600.19512587X-RAY DIFFRACTION99
3.8559-4.41320.16771350.16212624X-RAY DIFFRACTION98
4.4132-5.55750.18511390.15042662X-RAY DIFFRACTION98
5.5575-38.51510.23851260.17192749X-RAY DIFFRACTION98

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