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- PDB-6f85: Crystal structure of cytochrome P450 CYP260A1 (S276N) bound with ... -

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Basic information

Entry
Database: PDB / ID: 6f85
TitleCrystal structure of cytochrome P450 CYP260A1 (S276N) bound with histidine
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 / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / 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 / HISTIDINE / C-19 steroid 1alpha-hydroxylase
Similarity search - Component
Biological speciesSorangium cellulosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)90,5956
Polymers89,0502
Non-polymers1,5454
Water5,296294
1
A: Cytochrome P450 CYP260A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2983
Polymers44,5251
Non-polymers7732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 CYP260A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2983
Polymers44,5251
Non-polymers7732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.378, 64.382, 128.130
Angle α, β, γ (deg.)90.000, 112.610, 90.000
Int Tables number5
Space group name H-MC121

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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-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris propane pH 6.5, 14% (w/v) PEG 3350, 0.25 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: 2.05→46.33 Å / Num. obs: 47060 / % possible obs: 99.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 31.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.026 / Rrim(I) all: 0.054 / Net I/σ(I): 17.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.05-2.114.40.39535860.9170.2110.4598.7
8.94-46.333.90.0246070.9990.0130.02798

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Processing

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

5liv


Resolution: 2.05→46.33 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 22.98
RfactorNum. reflection% reflection
Rfree0.2133 4608 5 %
Rwork0.1816 --
obs0.1832 47060 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.08 Å2 / Biso mean: 36.4781 Å2 / Biso min: 18.18 Å2
Refinement stepCycle: final / Resolution: 2.05→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6100 0 194 294 6588
Biso mean--31 35.51 -
Num. residues----784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166473
X-RAY DIFFRACTIONf_angle_d1.4618831
X-RAY DIFFRACTIONf_chiral_restr0.065949
X-RAY DIFFRACTIONf_plane_restr0.0091152
X-RAY DIFFRACTIONf_dihedral_angle_d13.4132383
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 (%)
2.05-2.07330.29421540.24322878303299
2.0733-2.09770.2881790.2312820299999
2.0977-2.12330.26761470.22792944309199
2.1233-2.15020.26441370.22922958309599
2.1502-2.17840.27611600.22692867302799
2.1784-2.20830.24881470.22042985313299
2.2083-2.23980.27131310.21362852298399
2.2398-2.27330.22972030.20122897310099
2.2733-2.30880.23641600.19952911307199
2.3088-2.34660.25381210.19342930305199
2.3466-2.38710.28441270.20393018314599
2.3871-2.43050.29771280.19442851297999
2.4305-2.47730.22981720.19182932310498
2.4773-2.52780.20971300.18832870300099
2.5278-2.58280.25041800.19932936311699
2.5828-2.64280.28411830.20122825300899
2.6428-2.70890.27732060.19882941314799
2.7089-2.78220.27491220.20412898302099
2.7822-2.8640.24021470.202429813128100
2.864-2.95650.26281820.199628643046100
2.9565-3.06210.28311590.20132939309899
3.0621-3.18470.19551640.19732885304999
3.1847-3.32960.21010.19042986308799
3.3296-3.50510.17221100.177630233133100
3.5051-3.72460.21451370.16132901303899
3.7246-4.0120.17171460.153529433089100
4.012-4.41550.17572090.147628393048100
4.4155-5.05370.16481460.14442928307499
5.0537-6.36450.20071340.179429763110100
6.3645-46.34280.15651860.16192887307399

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