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- PDB-8gdi: X-ray crystal structure of CYP124A1 from Mycobacterium Marinum in... -

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Basic information

Entry
Database: PDB / ID: 8gdi
TitleX-ray crystal structure of CYP124A1 from Mycobacterium Marinum in complex with 7-ketocholesterol
ComponentsCytochrome P450 124A1
KeywordsOXIDOREDUCTASE / Cytochrome P450 / ligand bound
Function / homology
Function and homology information


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 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(3beta,8alpha,9beta)-3-hydroxycholest-5-en-7-one / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 124A1, Cyp124A1
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsGhith, A. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210103970 Australia
CitationJournal: J.Steroid Biochem.Mol.Biol. / Year: 2023
Title: The oxidation of cholesterol derivatives by the CYP124 and CYP142 enzymes from Mycobacterium marinum.
Authors: Ghith, A. / Bruning, J.B. / Bell, S.G.
History
DepositionMar 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 124A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3303
Polymers47,3131
Non-polymers1,0172
Water8,737485
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.548, 74.991, 95.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome P450 124A1 / Cyp124A1


Mass: 47313.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / Gene: cyp124A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2HHT9
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-0GV / (3beta,8alpha,9beta)-3-hydroxycholest-5-en-7-one / 7-ketocholesterol


Mass: 400.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.20 M ammonium sulfate, 20% w/v polyethylene glycol 3350, pH 6.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.81→37.5 Å / Num. obs: 44725 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.033 / Rrim(I) all: 0.123 / Χ2: 0.93 / Net I/σ(I): 13.8 / Num. measured all: 602711
Reflection shellResolution: 1.81→1.85 Å / % possible obs: 99.8 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.756 / Num. measured all: 36000 / Num. unique obs: 2599 / CC1/2: 0.907 / Rpim(I) all: 0.21 / Rrim(I) all: 0.785 / Χ2: 0.63 / Net I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→37.5 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 2180 4.88 %
Rwork0.1748 --
obs0.1763 44646 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3397 0 0 485 3882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083553
X-RAY DIFFRACTIONf_angle_d1.3684866
X-RAY DIFFRACTIONf_dihedral_angle_d17.678491
X-RAY DIFFRACTIONf_chiral_restr0.146522
X-RAY DIFFRACTIONf_plane_restr0.007638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.850.27921370.25382596X-RAY DIFFRACTION100
1.85-1.890.28091330.22722635X-RAY DIFFRACTION100
1.89-1.940.25541490.21072604X-RAY DIFFRACTION100
1.94-1.990.25441330.19892614X-RAY DIFFRACTION100
1.99-2.050.22981450.18622598X-RAY DIFFRACTION100
2.05-2.120.23591610.18722612X-RAY DIFFRACTION100
2.12-2.190.21111380.18452625X-RAY DIFFRACTION100
2.19-2.280.26931170.18492644X-RAY DIFFRACTION100
2.28-2.380.22551350.17432644X-RAY DIFFRACTION100
2.38-2.510.2381420.18372631X-RAY DIFFRACTION100
2.51-2.670.21321220.17992663X-RAY DIFFRACTION100
2.67-2.870.22351280.18542677X-RAY DIFFRACTION100
2.87-3.160.23291270.18022680X-RAY DIFFRACTION100
3.16-3.620.19381340.16672684X-RAY DIFFRACTION100
3.62-4.560.13541270.1492719X-RAY DIFFRACTION99
4.56-37.50.17111520.14962840X-RAY DIFFRACTION100

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