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- PDB-4uax: X-ray crystal structure of ligand free CYP142A2 from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 4uax
TitleX-ray crystal structure of ligand free CYP142A2 from Mycobacterium smegmatis
ComponentsP450 heme-thiolate protein
KeywordsOXIDOREDUCTASE / Cytochrome P450 / hemoprotein
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming] / 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, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsMadrona, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI074824 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM25515 United States
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Cholesterol ester oxidation by mycobacterial cytochrome p450.
Authors: Frank, D.J. / Madrona, Y. / Ortiz de Montellano, P.R.
History
DepositionAug 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.5Sep 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 / refine_hist
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: P450 heme-thiolate protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3962
Polymers45,7801
Non-polymers6161
Water10,611589
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-27 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.650, 83.518, 94.501
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 P450 heme-thiolate protein


Mass: 45780.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5918 / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / References: UniProt: A0R4Q6
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.54 Å3/Da / Density % sol: 51.6 % / Description: Rectangular
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1.27 M sodium citrate dibasic, 60 mM calcium chloride, 100 mM Bis-Tris propane, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2014
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 1.78→19.591 Å / Num. obs: 42943 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Redundancy: 2.79 % / Rsym value: 0.096 / Net I/σ(I): 16.05
Reflection shellResolution: 1.78→1.89 Å / Redundancy: 4.35 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.95 / % possible all: 89.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ZBY

3zby


Resolution: 1.78→19.591 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 2148 5.01 %Random
Rwork0.1669 ---
obs0.1684 42890 98.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→19.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 43 589 3780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113267
X-RAY DIFFRACTIONf_angle_d1.0834442
X-RAY DIFFRACTIONf_dihedral_angle_d13.4431216
X-RAY DIFFRACTIONf_chiral_restr0.043489
X-RAY DIFFRACTIONf_plane_restr0.005586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7796-1.8210.24911030.24612174X-RAY DIFFRACTION80
1.821-1.86650.26171540.21852581X-RAY DIFFRACTION96
1.8665-1.91690.25591300.20062728X-RAY DIFFRACTION100
1.9169-1.97330.21251360.18632727X-RAY DIFFRACTION99
1.9733-2.03690.20981440.17262744X-RAY DIFFRACTION100
2.0369-2.10960.1931560.17822700X-RAY DIFFRACTION100
2.1096-2.1940.20041520.16332746X-RAY DIFFRACTION100
2.194-2.29370.17111190.16052768X-RAY DIFFRACTION100
2.2937-2.41440.19821390.16482732X-RAY DIFFRACTION100
2.4144-2.56540.20421430.17062781X-RAY DIFFRACTION100
2.5654-2.76290.21841570.1732746X-RAY DIFFRACTION100
2.7629-3.040.2231390.17422783X-RAY DIFFRACTION100
3.04-3.47780.18571420.15842812X-RAY DIFFRACTION100
3.4778-4.37360.1551520.13832824X-RAY DIFFRACTION100
4.3736-19.59240.17371820.15152896X-RAY DIFFRACTION99

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