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- PDB-7q9e: CYP106A1 -

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Basic information

Entry
Database: PDB / ID: 7q9e
TitleCYP106A1
ComponentsCytochrome P450
KeywordsBIOSYNTHETIC PROTEIN / Cytochrome P450 / Steroid dehydrogenation
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / 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 / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / HYDROGEN PEROXIDE / Cytochrome P450
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCarius, Y. / Hutter, M. / Kiss, F. / Bernhardt, R. / Lancaster, C.R.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other government Germany
CitationJournal: Febs Lett. / Year: 2022
Title: Structural comparison of the cytochrome P450 enzymes CYP106A1 and CYP106A2 provides insight into their differences in steroid conversion.
Authors: Carius, Y. / Hutter, M. / Kiss, F. / Bernhardt, R. / Lancaster, C.R.D.
History
DepositionNov 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450
B: Cytochrome P450
C: Cytochrome P450
D: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,50833
Polymers193,8394
Non-polymers4,66929
Water18,4111022
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6538
Polymers48,4601
Non-polymers1,1937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,85911
Polymers48,4601
Non-polymers1,39910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6709
Polymers48,4601
Non-polymers1,2108
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3275
Polymers48,4601
Non-polymers8684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.690, 82.870, 84.860
Angle α, β, γ (deg.)95.360, 90.000, 90.000
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cytochrome P450


Mass: 48459.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (strain DSM 319) (bacteria)
Strain: DSM 319 / Gene: BMD_1855 / Production host: Escherichia coli (E. coli)
References: UniProt: D5DF35, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one ...References: UniProt: D5DF35, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor

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Non-polymers , 8 types, 1051 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#7: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#8: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1022 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, lithium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.97916 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.7→25.92 Å / Num. obs: 168988 / % possible obs: 88.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.043 / Rrim(I) all: 0.079 / Net I/σ(I): 7.05
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 23968 / CC1/2: 0.92 / Rpim(I) all: 0.199 / Rrim(I) all: 0.367

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YT3

4yt3


Resolution: 1.7→25.82 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.118 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 8441 5 %RANDOM
Rwork0.1689 ---
obs0.1707 160539 88.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.25 Å2 / Biso mean: 22.634 Å2 / Biso min: 7.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20.04 Å20.23 Å2
2---0.83 Å2-1.32 Å2
3----0.6 Å2
Refinement stepCycle: final / Resolution: 1.7→25.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12597 0 285 1022 13904
Biso mean--28.97 30.75 -
Num. residues----1558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01313342
X-RAY DIFFRACTIONr_bond_other_d0.0020.01712027
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.66618198
X-RAY DIFFRACTIONr_angle_other_deg1.4831.58227915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69551595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87922.619737
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.781152187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3911578
X-RAY DIFFRACTIONr_chiral_restr0.0890.21714
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214902
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022932
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 583 -
Rwork0.236 10873 -
all-11456 -
obs--81.68 %

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