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- PDB-6cvc: Mycobacterium marinum cytochrome P450 CYP124A1 in the substrate-f... -

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Basic information

Entry
Database: PDB / ID: 6cvc
TitleMycobacterium marinum cytochrome P450 CYP124A1 in the substrate-free form
ComponentsCytochrome P450 124A1, Cyp124A1
KeywordsOXIDOREDUCTASE / cytochrome P450 / monooxygenase / heme protein
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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 124A1, Cyp124A1
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsChild, S.A. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT140100355 Australia
CitationJournal: To Be Published
Title: A comparison of the steroid binding cytochrome P450s from Mycobacterium marinum and Mycobacterium tuberculosis
Authors: Child, S.A. / Bruning, J.B. / Bell, S.G.
History
DepositionMar 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: 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 124A1, Cyp124A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3655
Polymers48,4611
Non-polymers9054
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-61 kcal/mol
Surface area17240 Å2
2
A: Cytochrome P450 124A1, Cyp124A1
hetero molecules

A: Cytochrome P450 124A1, Cyp124A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,73110
Polymers96,9212
Non-polymers1,8098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5520 Å2
ΔGint-136 kcal/mol
Surface area32560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.776, 72.359, 65.602
Angle α, β, γ (deg.)90.000, 109.720, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-866-

HOH

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Components

#1: Protein Cytochrome P450 124A1, Cyp124A1


Mass: 48460.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: cyp124A1, MMAR_3361 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.34 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.26 M ammonium sulphate, 20% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→46.49 Å / Num. obs: 21973 / % possible obs: 99.1 % / Redundancy: 7.4 % / Biso Wilson estimate: 19.04 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.298 / Rpim(I) all: 0.118 / Rrim(I) all: 0.321 / Net I/σ(I): 7.7 / Num. measured all: 163114 / Scaling rejects: 342
Reflection shell

Diffraction-ID: 1 / % possible all: 98.5

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.2-2.277.11.1351354419060.8550.461.2263.1
9.07-46.496.50.06821593330.9940.0290.07418.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimless0.6.2data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wm5

2wm5


Resolution: 2.2→25.193 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 1070 4.88 %Random selection
Rwork0.2043 20848 --
obs0.2067 21918 98.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.59 Å2 / Biso mean: 29.4643 Å2 / Biso min: 4.4 Å2
Refinement stepCycle: final / Resolution: 2.2→25.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 58 297 3685
Biso mean--24.1 32.25 -
Num. residues----422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023518
X-RAY DIFFRACTIONf_angle_d0.4594809
X-RAY DIFFRACTIONf_chiral_restr0.036511
X-RAY DIFFRACTIONf_plane_restr0.003632
X-RAY DIFFRACTIONf_dihedral_angle_d16.862066
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.30010.43631320.40142543267597
2.3001-2.42130.30331440.25812573271799
2.4213-2.57280.27571400.22492588272899
2.5728-2.77130.27621310.20672596272799
2.7713-3.04970.25961450.20722622276799
3.0497-3.490.231110.19282620273199
3.49-4.39330.20941320.15942628276099
4.3933-25.19420.19981350.15952678281399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9952-0.02960.350.5699-0.09770.98430.0374-0.327-0.19430.06570.11920.13290.0054-0.2978-0.13950.1833-0.0193-0.02160.260.08230.219516.77620.799821.0531
20.80310.07580.49131.31730.46871.55890.08830.0342-0.2126-0.04220.1249-0.23620.32410.1309-0.15710.22340.0248-0.03330.1155-0.01670.185435.7858-8.84865.7472
31.03-0.08180.42331.03260.23651.32120.0027-0.0975-0.0423-0.05620.04090.0772-0.0023-0.0588-0.03430.1593-0.0153-0.00250.07810.02790.139525.10950.57239.957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 130 )A7 - 130
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 208 )A131 - 208
3X-RAY DIFFRACTION3chain 'A' and (resid 209 through 428 )A209 - 428

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