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- PDB-5dqn: Polyethylene 600-bound form of P450 CYP125A3 mutant from Myobacte... -

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Basic information

Entry
Database: PDB / ID: 5dqn
TitlePolyethylene 600-bound form of P450 CYP125A3 mutant from Myobacterium Smegmatis - W83Y
ComponentsCytochrome P450 CYP125
KeywordsOXIDOREDUCTASE / CHOLESTEROL METABOLISM
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / cholest-4-en-3-one 26-monooxygenase 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
CITRIC ACID / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Steroid C26-monooxygenase / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.262 Å
AuthorsOrtiz de Montellano, P.J. / Frank, D.J. / Waddling, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI074824 United States
CitationJournal: Biochemistry / Year: 2015
Title: Cytochrome P450 125A4, the Third Cholesterol C-26 Hydroxylase from Mycobacterium smegmatis.
Authors: Frank, D.J. / Waddling, C.A. / La, M. / Ortiz de Montellano, P.R.
History
DepositionSep 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

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Assembly

Deposited unit
A: Cytochrome P450 CYP125
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2346
Polymers46,9971
Non-polymers1,2375
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-42 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.821, 108.821, 118.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450 CYP125


Mass: 46996.734 Da / Num. of mol.: 1 / Mutation: W83Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: cyp125, MSMEI_5834 / Plasmid: PCW / Production host: Escherichia coli (E. coli) / Strain (production host): DH5(Alpha)
References: UniProt: I7G9K1, UniProt: A0R4Y3*PLUS, EC: 1.14.13.151

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Non-polymers , 5 types, 91 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 67.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: Well contents (JCSG Core-III screen, G4): 0.1M Phosphate-Citrate buffer, pH 4.2 PEG 600, 40% v/v Drop Contents: 90% Well contents (see above) 10% Silver Bullets screen, B18: - 0.33% w/v 2,6- ...Details: Well contents (JCSG Core-III screen, G4): 0.1M Phosphate-Citrate buffer, pH 4.2 PEG 600, 40% v/v Drop Contents: 90% Well contents (see above) 10% Silver Bullets screen, B18: - 0.33% w/v 2,6-Naphthalenedisulfonic acid disodium salt - 0.33% w/v 2-Aminobenzenedisulfonic acid - 0.33% w/v m-Benzenedisulfonic acid disodium salt 0.02M HEPES sodium, pH 6.8

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11585 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11585 Å / Relative weight: 1
ReflectionResolution: 1.76→80.322 Å / Num. obs: 32185 / % possible obs: 99.67 % / Redundancy: 2 % / Biso Wilson estimate: 51.5 Å2 / Rmerge(I) obs: 0.04274 / Net I/σ(I): 19.37

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLM7.0.1data reduction
SCALA3.2.5data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4APY

4apy


Resolution: 2.262→80.247 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0.95 / Phase error: 23.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 3099 4.91 %Random selection
Rwork0.1646 ---
obs0.1668 32185 99.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.4 Å2
Refinement stepCycle: LAST / Resolution: 2.262→80.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 82 86 3374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043421
X-RAY DIFFRACTIONf_angle_d0.7994659
X-RAY DIFFRACTIONf_dihedral_angle_d13.0491278
X-RAY DIFFRACTIONf_chiral_restr0.03489
X-RAY DIFFRACTIONf_plane_restr0.004619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2621-2.29750.34721400.33292551X-RAY DIFFRACTION93
2.2975-2.33510.35561380.30422779X-RAY DIFFRACTION99
2.3351-2.37540.31831600.28252688X-RAY DIFFRACTION99
2.3754-2.41860.34171200.26542720X-RAY DIFFRACTION99
2.4186-2.46510.32041370.26092747X-RAY DIFFRACTION99
2.4651-2.51540.24431600.22992680X-RAY DIFFRACTION99
2.5154-2.57010.2721340.22992719X-RAY DIFFRACTION99
2.5701-2.62990.23691500.21472773X-RAY DIFFRACTION99
2.6299-2.69570.30551460.20932732X-RAY DIFFRACTION99
2.6957-2.76860.23851360.19232736X-RAY DIFFRACTION99
2.7686-2.850.23841490.18522725X-RAY DIFFRACTION100
2.85-2.9420.25121260.18232785X-RAY DIFFRACTION100
2.942-3.04720.2051290.17732709X-RAY DIFFRACTION99
3.0472-3.16920.22581230.1832732X-RAY DIFFRACTION100
3.1692-3.31340.22531330.19012783X-RAY DIFFRACTION100
3.3134-3.48810.19151610.15122740X-RAY DIFFRACTION100
3.4881-3.70670.18371470.14992732X-RAY DIFFRACTION100
3.7067-3.99290.18481360.13512757X-RAY DIFFRACTION100
3.9929-4.39470.15681350.12322756X-RAY DIFFRACTION100
4.3947-5.03050.12651370.12372724X-RAY DIFFRACTION100
5.0305-6.33750.25411490.15792745X-RAY DIFFRACTION100
6.3375-80.29770.19531530.14382742X-RAY DIFFRACTION100
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)
11.79530.4403-0.63092.7733-1.05662.59470.0219-0.0946-0.1169-0.00210.04850.07520.1316-0.0888-0.07660.3107-0.0214-0.00950.36690.00570.336612.4743-20.4213-2.188
23.04560.99052.2944.10483.18673.2890.00950.21930.4716-0.13070.0507-0.4876-0.94130.7942-0.03520.5571-0.16380.05090.5135-0.06210.756131.84647.84070.0708
32.7584-0.8131.48822.1188-0.31682.58580.0486-0.19170.23590.0626-0.0228-0.0626-0.3964-0.05680.00870.5033-0.07150.07080.4293-0.05570.456718.49442.1845-0.7351
42.06390.4135-0.44832.2497-0.21221.96590.026-0.1718-0.00540.14030.0036-0.3483-0.07890.4623-0.05230.3328-0.0063-0.00920.47130.02260.349426.3354-13.91091.7426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 119 )
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 144 )
3X-RAY DIFFRACTION3chain 'A' and (resid 145 through 280 )
4X-RAY DIFFRACTION4chain 'A' and (resid 281 through 411 )

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