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- PDB-8abs: Crystal structure of CYP109A2 from Bacillus megaterium bound with... -

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Basic information

Entry
Database: PDB / ID: 8abs
TitleCrystal structure of CYP109A2 from Bacillus megaterium bound with testosterone and putative ligand 4,6-dimethyloctanoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Testosterone / Fatty acid / Steroid / Complex
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / 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
HEME B/C / TESTOSTERONE / (4~{S},6~{S})-4,6-dimethyloctanoic acid / Cytochrome P450
Similarity search - Component
Biological speciesPriestia megaterium DSM 319 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsJozwik, I.K. / Rozeboom, H.J. / Thunnissen, A.-M.W.H.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Commission289217European Union
European Commission722610European Union
CitationJournal: Febs J. / Year: 2023
Title: Regio- and stereoselective steroid hydroxylation by CYP109A2 from Bacillus megaterium explored by X-ray crystallography and computational modeling.
Authors: Jozwik, I.K. / Bombino, E. / Abdulmughni, A. / Hartz, P. / Rozeboom, H.J. / Wijma, H.J. / Kappl, R. / Janssen, D.B. / Bernhardt, R. / Thunnissen, A.W.H.
History
DepositionJul 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: 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 1.2Oct 25, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_validate_chiral
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,64210
Polymers46,9861
Non-polymers1,6569
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-87 kcal/mol
Surface area17110 Å2
Unit cell
Length a, b, c (Å)78.030, 78.030, 187.857
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450


Mass: 46986.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium DSM 319 (bacteria) / Strain: DSM 319 / Gene: BMD_2035 / Production host: Escherichia coli (E. coli)
References: UniProt: D5DF88, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

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Non-polymers , 5 types, 158 molecules

#2: Chemical ChemComp-HEB / HEME B/C / HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-W2L / (4~{S},6~{S})-4,6-dimethyloctanoic acid


Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TES / TESTOSTERONE


Mass: 288.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein was concentrated to 33 mg/ml in 50 mM citrate buffer, pH 5.5, 0.1 mM testosterone. The crystallization reservoir solution contained 0.4-0.55 M ammonium sulfate, 1.05-1.2 M lithium ...Details: Protein was concentrated to 33 mg/ml in 50 mM citrate buffer, pH 5.5, 0.1 mM testosterone. The crystallization reservoir solution contained 0.4-0.55 M ammonium sulfate, 1.05-1.2 M lithium sulfate and 0.1 M sodium citrate buffer, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.75→48.84 Å / Num. obs: 59408 / % possible obs: 99.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 35.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.025 / Rrim(I) all: 0.059 / Net I/σ(I): 13.9 / Num. measured all: 335918 / Scaling rejects: 217
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
1.75-1.785.81.7971862032150.4910.8131.9771100
9.09-48.844.70.02924725270.9990.0150.03342.198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OFQ

5ofq


Resolution: 1.75→48.84 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 21.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 3027 5.11 %
Rwork0.188 56255 -
obs0.1889 59282 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.01 Å2 / Biso mean: 50.0764 Å2 / Biso min: 28.24 Å2
Refinement stepCycle: final / Resolution: 1.75→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 183 149 3507
Biso mean--52.21 46.05 -
Num. residues----394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.780.35261210.339825342655100
1.78-1.810.32691460.308224842630100
1.81-1.840.29581270.294525102637100
1.84-1.870.27451500.274525182668100
1.87-1.910.30311470.25124972644100
1.91-1.950.21821550.232424942649100
1.95-1.990.25861220.22325332655100
1.99-2.030.23141490.226725102659100
2.03-2.090.25361520.229825282680100
2.09-2.140.24481150.190225372652100
2.14-2.20.19831370.180125352672100
2.2-2.280.21031320.165625302662100
2.28-2.360.1971380.172525572695100
2.36-2.450.22581280.18225682696100
2.45-2.560.22011460.189525412687100
2.56-2.70.2451260.208625822708100
2.7-2.870.20671370.189225602697100
2.87-3.090.19591400.196825732713100
3.09-3.40.21041480.19125872735100
3.4-3.890.18651300.164126232753100
3.89-4.90.15961270.15162653278099
4.9-48.840.20581540.19792801295599
Refinement TLS params.Method: refined / Origin x: 14.2027 Å / Origin y: -8.6148 Å / Origin z: 16.9267 Å
111213212223313233
T0.2441 Å2-0.0393 Å2-0.0209 Å2-0.4156 Å20.0533 Å2--0.3029 Å2
L1.25 °2-0.2855 °20.3319 °2-1.1812 °2-0.2945 °2--1.0514 °2
S-0.0759 Å °-0.0454 Å °0.0786 Å °0.0333 Å °0.0049 Å °-0.1015 Å °-0.1344 Å °0.1056 Å °0.0676 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 401
2X-RAY DIFFRACTION1allA501 - 503
3X-RAY DIFFRACTION1allB1 - 6
4X-RAY DIFFRACTION1allD2 - 164

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