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- PDB-6f88: Crystal structure of cytochrome P450 CYP260A1 (S276N) bound with ... -

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Basic information

Entry
Database: PDB / ID: 6f88
TitleCrystal structure of cytochrome P450 CYP260A1 (S276N) bound with progesterone
ComponentsCytochrome P450 CYP260A1
KeywordsOXIDOREDUCTASE / Bacterial Proteins / Sorangium cellulosum / Cytochrome P-450 Enzyme System / Cytochrome P450 / Hydroxylation / Heme / Oxidation-Reduction / Progesterone / Histidine / Biocatalysis
Function / homology
Function and homology information


C-19 steroid 1alpha-hydroxylase / 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 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PROGESTERONE / C-19 steroid 1alpha-hydroxylase
Similarity search - Component
Biological speciesSorangium cellulosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsJozwik, I.K. / Thunnissen, A.M.W.H.
Funding support Germany, Netherlands, 2items
OrganizationGrant numberCountry
German Research FoundationBE 1343/23-1/23-2 Germany
European Commission289217 Netherlands
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Structure-Based Engineering of Steroidogenic CYP260A1 for Stereo- and Regioselective Hydroxylation of Progesterone.
Authors: Khatri, Y. / Jozwik, I.K. / Ringle, M. / Ionescu, I.A. / Litzenburger, M. / Hutter, M.C. / Thunnissen, A.W.H. / Bernhardt, R.
History
DepositionDec 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: 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 CYP260A1
B: Cytochrome P450 CYP260A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9126
Polymers89,0502
Non-polymers1,8624
Water12,178676
1
A: Cytochrome P450 CYP260A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4563
Polymers44,5251
Non-polymers9312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 CYP260A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4563
Polymers44,5251
Non-polymers9312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.886, 65.824, 128.963
Angle α, β, γ (deg.)90.000, 112.840, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-851-

HOH

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Components

#1: Protein Cytochrome P450 CYP260A1


Mass: 44524.922 Da / Num. of mol.: 2 / Mutation: S276N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorangium cellulosum (strain So ce56) (bacteria)
Strain: So ce56 / Gene: sce1588 / Plasmid: pET22b / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): C43
References: UniProt: A9FDB7, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-STR / PROGESTERONE


Mass: 314.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30O2 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris propane pH 6.5, 17% (w/v) PEG 3350, 0.02 M NaNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.75→46.49 Å / Num. obs: 78316 / % possible obs: 99.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 21.05 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.02 / Rrim(I) all: 0.042 / Net I/σ(I): 24.3 / Num. measured all: 351321
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.75-1.784.60.41972042980.8660.2090.4543.899.5
9.09-46.494.40.0226025860.9990.0110.02377.997.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
EDNAdata collection
XDSdata reduction
Aimless0.5.1data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5liv

5liv


Resolution: 1.75→46.489 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 19.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 7588 4.94 %
Rwork0.1674 145960 -
obs0.1692 78316 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.18 Å2 / Biso mean: 26.6988 Å2 / Biso min: 9.66 Å2
Refinement stepCycle: final / Resolution: 1.75→46.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6128 0 175 677 6980
Biso mean--17.27 33.02 -
Num. residues----787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146496
X-RAY DIFFRACTIONf_angle_d1.4548866
X-RAY DIFFRACTIONf_chiral_restr0.177963
X-RAY DIFFRACTIONf_plane_restr0.0091155
X-RAY DIFFRACTIONf_dihedral_angle_d13.3542402
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.76990.29692760.2524966524299
1.7699-1.79070.25552300.246748695099100
1.7907-1.81260.29272810.24034831511299
1.8126-1.83550.2472490.23664814506399
1.8355-1.85970.25022480.21634852510099
1.8597-1.88510.27512730.21649125185100
1.8851-1.91210.26542550.221647715026100
1.9121-1.94060.25252710.20824949522099
1.9406-1.97090.24281860.20194803498999
1.9709-2.00320.21332790.19164921520099
2.0032-2.03780.24142820.19214713499599
2.0378-2.07480.242220.18914976519899
2.0748-2.11470.18462140.17864828504299
2.1147-2.15790.21523320.176148355167100
2.1579-2.20480.19162740.170948775151100
2.2048-2.25610.17982260.1648595085100
2.2561-2.31250.16892760.157349255201100
2.3125-2.37510.20042500.159947935043100
2.3751-2.44490.19722380.156848985136100
2.4449-2.52390.20912320.15849455177100
2.5239-2.61410.18582180.162248805098100
2.6141-2.71870.22422520.1654850510299
2.7187-2.84240.22630.16884863512699
2.8424-2.99230.20843000.17994822512299
2.9923-3.17970.23072340.16774846508099
3.1797-3.42510.21442380.168648535091100
3.4251-3.76970.19892760.148749185194100
3.7697-4.31480.15172140.135549025116100
4.3148-5.43490.1712390.13424853509299
5.4349-46.50560.18622600.16294836509699

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