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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


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / 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

Downloads & links

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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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