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- PDB-6mcw: Crystal structure of the P450 domain of the CYP51-ferredoxin fusi... -

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Basic information

Entry
Database: PDB / ID: 6mcw
TitleCrystal structure of the P450 domain of the CYP51-ferredoxin fusion protein from Methylococcus capsulatus, complex with the detergent Anapoe-X-114
ComponentsCytochrome P450 51
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 FOLD / CYP51 / HEME / STEROL BIOSYNTHESIS
Function / homology
Function and homology information


sterol 14alpha-demethylase / steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / bile acid biosynthetic process / cholesterol homeostasis / iron ion binding / heme binding
Similarity search - Function
4Fe-4S single cluster domain / Cytochrome P450, E-class, group IV / Cytochrome p450 / Cytochrome P450 / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-JDJ / Cytochrome P450 51
Similarity search - Component
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHargrove, T. / Wawrzak, Z. / Lamb, D.C. / Lepesheva, G.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01067871 United States
CitationJournal: Mol.Biol.Evol. / Year: 2020
Title: Concerning P450 evolution: Structural Analyses Support Bacterial Origin of Sterol 14 alpha-Demethylases.
Authors: Lamb, D.C. / Hargrove, T.Y. / Zhao, B. / Wawrzak, Z. / Goldstone, J.V. / Nes, W.D. / Kelly, S.L. / Waterman, M.R. / Stegeman, J.J. / Lepesheva, G.I.
History
DepositionSep 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 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 51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6593
Polymers62,4841
Non-polymers1,1752
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.685, 150.685, 66.321
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cytochrome P450 51


Mass: 62483.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) (bacteria)
Strain: ATCC 33009 / NCIMB 11132 / Bath / Gene: cyp51, MCA2711 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS-164 / References: UniProt: Q603T8, sterol 14alpha-demethylase
#2: Chemical ChemComp-JDJ / 23-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]-3,6,9,12,15,18,21-heptaoxatricosan-1-ol / Anapoe-X-114


Mass: 558.744 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H54O9
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.48 Å3/Da / Density % sol: 64.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.4 / Details: PEG 6000, photassium phosphate, glycerol, TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07807 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2018 / Details: FOCUSING MIRRORS
RadiationMonochromator: SI (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07807 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 33877 / % possible obs: 99 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.043 / Rrim(I) all: 0.109 / Net I/σ(I): 17.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.873 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1681 / Rpim(I) all: 0.575 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FMO

6fmo


Resolution: 2.4→29.96 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.609 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.197 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23722 1673 4.9 %RANDOM
Rwork0.21582 ---
obs0.21689 32189 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.303 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0.41 Å2-0 Å2
2---0.83 Å20 Å2
3---2.68 Å2
Refinement stepCycle: 1 / Resolution: 2.4→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3609 0 79 36 3724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0143781
X-RAY DIFFRACTIONr_bond_other_d00.0173412
X-RAY DIFFRACTIONr_angle_refined_deg0.8211.6965122
X-RAY DIFFRACTIONr_angle_other_deg0.8171.6548006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2565445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.99320.045223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.60115649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3081542
X-RAY DIFFRACTIONr_chiral_restr0.2530.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024238
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02702
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.3115.6291783
X-RAY DIFFRACTIONr_mcbond_other5.2995.6261782
X-RAY DIFFRACTIONr_mcangle_it7.798.4432227
X-RAY DIFFRACTIONr_mcangle_other7.7888.4472228
X-RAY DIFFRACTIONr_scbond_it6.076.3821996
X-RAY DIFFRACTIONr_scbond_other6.0716.3841994
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.9619.2832893
X-RAY DIFFRACTIONr_long_range_B_refined12.94467.1064238
X-RAY DIFFRACTIONr_long_range_B_other12.94667.14236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 105 -
Rwork0.351 2405 -
obs--99.92 %

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