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- PDB-6f8c: Crystal structure of cytochrome P450 CYP260A1 (S276I) bound with ... -

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Basic information

Entry
Database: PDB / ID: 6f8c
TitleCrystal structure of cytochrome P450 CYP260A1 (S276I) 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: 1.9 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)90,9106
Polymers89,0482
Non-polymers1,8624
Water7,512417
1
A: Cytochrome P450 CYP260A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4553
Polymers44,5241
Non-polymers9312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 CYP260A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4553
Polymers44,5241
Non-polymers9312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.907, 64.565, 128.644
Angle α, β, γ (deg.)90.000, 113.070, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cytochrome P450 CYP260A1


Mass: 44523.977 Da / Num. of mol.: 2 / Mutation: S276I
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.: 417 / 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: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris propane pH 6.5, 19% (w/v) PEG 3350, 0.05 M MgCl2

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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: 1.9→46.42 Å / Num. obs: 59758 / % possible obs: 99.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.023 / Rrim(I) all: 0.048 / Net I/σ(I): 21.7 / Num. measured all: 249859
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.3 % / % possible all: 99.2

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.9-1.940.4211653838590.860.2280.4813.6
9.11-46.420.01924905840.9990.010.02269.8

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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: 1.9→46.418 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 23.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 5655 4.83 %
Rwork0.1871 111309 -
obs0.1891 59758 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.72 Å2 / Biso mean: 32.4238 Å2 / Biso min: 12.23 Å2
Refinement stepCycle: final / Resolution: 1.9→46.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6138 0 132 418 6688
Biso mean--26.48 35.32 -
Num. residues----788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166444
X-RAY DIFFRACTIONf_angle_d1.4498778
X-RAY DIFFRACTIONf_chiral_restr0.076965
X-RAY DIFFRACTIONf_plane_restr0.0091145
X-RAY DIFFRACTIONf_dihedral_angle_d15.3682388
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 (%)
1.9-1.92160.30181620.26973826398899
1.9216-1.94420.30321960.26413655385199
1.9442-1.96790.29671740.26843671384599
1.9679-1.99280.33132000.2533762396299
1.9928-2.0190.27022310.23543711394299
2.019-2.04670.26091970.23793607380499
2.0467-2.07590.25721760.23033781395799
2.0759-2.10690.27491920.2263664385699
2.1069-2.13990.27731800.22633757393799
2.1399-2.17490.27912330.22933562379599
2.1749-2.21240.24131770.21423753393099
2.2124-2.25270.23621770.203537243901100
2.2527-2.2960.24612090.194636943903100
2.296-2.34290.28031540.1933712386699
2.3429-2.39380.2552080.20583765397399
2.3938-2.44950.26381720.195236433815100
2.4495-2.51070.23892180.1937503968100
2.5107-2.57860.23751490.19737833932100
2.5786-2.65450.21531690.20033689385899
2.6545-2.74020.24241800.19793747392799
2.7402-2.83810.2582150.20753612382799
2.8381-2.95170.2891380.215238053943100
2.9517-3.0860.26042020.20743674387699
3.086-3.24870.24031950.18873711390699
3.2487-3.45210.2222060.18353689389599
3.4521-3.71860.21662200.16993665388599
3.7186-4.09260.18981540.15553727388199
4.0926-4.68430.19042080.139737113919100
4.6843-5.89980.15591790.150337703949100
5.8998-46.43210.17741840.15553689387399

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