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

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Basic information

Entry
Database: PDB / ID: 8abr
TitleCrystal structure of CYP109A2 from Bacillus megaterium bound with putative ligands hexanoic acid and octanoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 monooxygenase / Complex / Fatty acid / Steroid hydroxylation
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
HEXANOIC ACID / HEME B/C / OCTANOIC ACID (CAPRYLIC ACID) / Cytochrome P450
Similarity search - Component
Biological speciesPriestia megaterium DSM 319 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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: Data collection / Database references / Category: citation / citation_author / diffrn_source
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 / _diffrn_source.pdbx_synchrotron_site
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)48,44210
Polymers46,9861
Non-polymers1,4559
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-81 kcal/mol
Surface area17280 Å2
Unit cell
Length a, b, c (Å)78.665, 78.665, 188.019
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, 105 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-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O2 / 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.: 96 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 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: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→94.01 Å / Num. obs: 35461 / % possible obs: 100 % / Redundancy: 26 % / Biso Wilson estimate: 55.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.013 / Rrim(I) all: 0.066 / Net I/σ(I): 27.6 / Num. measured all: 922831 / Scaling rejects: 2
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
2.1-2.1627.52.9357780828300.6950.5672.991.5100
8.91-94.01210.0221205757510.0050.022124.299.9

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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: 2.1→41.6 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.28 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 1771 5.01 %
Rwork0.1962 33590 -
obs0.1976 35361 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.3 Å2 / Biso mean: 71.9354 Å2 / Biso min: 44.8 Å2
Refinement stepCycle: final / Resolution: 2.1→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 147 96 3413
Biso mean--71.98 59.99 -
Num. residues----393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.160.30931360.285725112647
2.16-2.220.29661490.261425222671
2.22-2.290.25731200.243225492669
2.29-2.370.23851250.237925622687
2.37-2.470.2691430.220125182661
2.47-2.580.26631580.213725322690
2.58-2.720.24631210.212125812702
2.72-2.890.24541520.235325382690
2.89-3.110.28691300.243625692699
3.11-3.420.27371340.214926042738
3.42-3.920.19371290.194126222751
3.92-4.930.19671280.161426682796
4.94-41.60.21061460.180428142960
Refinement TLS params.Method: refined / Origin x: 14.1242 Å / Origin y: -8.9434 Å / Origin z: 17.0145 Å
111213212223313233
T0.4841 Å2-0.0334 Å2-0.0177 Å2-0.6831 Å20.0651 Å2--0.5462 Å2
L2.1085 °2-0.4534 °20.4923 °2-1.4007 °2-0.3164 °2--1.3809 °2
S-0.0991 Å °-0.0292 Å °0.1564 Å °0.0279 Å °0.0184 Å °-0.1009 Å °-0.2136 Å °0.1292 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 401
2X-RAY DIFFRACTION1allA501 - 503
3X-RAY DIFFRACTION1allB1 - 6
4X-RAY DIFFRACTION1allS1 - 97

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