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- PDB-3zby: Ligand-free structure of CYP142 from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 3zby
TitleLigand-free structure of CYP142 from Mycobacterium smegmatis
ComponentsP450 HEME-THIOLATE PROTEIN
KeywordsOXIDOREDUCTASE / CYP142 / CHOLESTEROL METABOLISM
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
beta-cyclodextrin / PROTOPORPHYRIN IX CONTAINING FE / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsGarcia-Fernandez, E. / Frank, D.J. / Galan, B. / Kells, P.M. / Podust, L.M. / Garcia, J.L. / Ortiz de Montellano, P.R.
CitationJournal: Environ.Microbiol. / Year: 2013
Title: A Highly Conserved Mycobacterial Cholesterol Catabolic Pathway.
Authors: Garcia-Fernandez, E. / Frank, D.J. / Galan, B. / Kells, P.M. / Podust, L.M. / Garcia, J.L. / Ortiz de Montellano, P.R.
History
DepositionNov 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Aug 14, 2013Group: Database references
Revision 1.3Feb 7, 2018Group: Database references / Source and taxonomy / Category: citation_author / entity_src_gen
Item: _citation_author.name / _entity_src_gen.gene_src_strain ..._citation_author.name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: P450 HEME-THIOLATE PROTEIN
B: P450 HEME-THIOLATE PROTEIN
C: P450 HEME-THIOLATE PROTEIN
D: P450 HEME-THIOLATE PROTEIN
E: P450 HEME-THIOLATE PROTEIN
F: P450 HEME-THIOLATE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,30241
Polymers274,6806
Non-polymers12,62235
Water47,5062637
1
C: P450 HEME-THIOLATE PROTEIN
F: P450 HEME-THIOLATE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,80014
Polymers91,5602
Non-polymers4,23912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-150.8 kcal/mol
Surface area33090 Å2
MethodPISA
2
B: P450 HEME-THIOLATE PROTEIN
E: P450 HEME-THIOLATE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,80014
Polymers91,5602
Non-polymers4,23912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-132.3 kcal/mol
Surface area32960 Å2
MethodPISA
3
A: P450 HEME-THIOLATE PROTEIN
hetero molecules

A: P450 HEME-THIOLATE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,60712
Polymers91,5602
Non-polymers4,04710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area5320 Å2
ΔGint-113.3 kcal/mol
Surface area32680 Å2
MethodPISA
4
D: P450 HEME-THIOLATE PROTEIN
hetero molecules

D: P450 HEME-THIOLATE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,80014
Polymers91,5602
Non-polymers4,23912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area5650 Å2
ΔGint-131.3 kcal/mol
Surface area33190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.051, 162.847, 266.443
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-7-

GLC

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Components

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Protein / Sugars , 2 types, 12 molecules ABCDEF

#1: Protein
P450 HEME-THIOLATE PROTEIN / CYP142A2


Mass: 45780.012 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: 6XHIS TAG ENGINEERED AT C-TERMINUS
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Plasmid: PCW / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: A0R4Q6
#2: Polysaccharide
Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0

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Non-polymers , 4 types, 2666 molecules

#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2637 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details1,2-ETHANEDIOL (EDO): CRYO-PROTECTANT PROTOPORPHYRIN IX CONTAINING FE (HEM): FE THIOLATE BOND TO ...1,2-ETHANEDIOL (EDO): CRYO-PROTECTANT PROTOPORPHYRIN IX CONTAINING FE (HEM): FE THIOLATE BOND TO CYS 343 SULFATE ION (SO4): PART OF CRYSTALLIZATION CONDITIONS
Sequence details6XHIS TAG ENGINEERED AT C-TERMINUS

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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: 3.68 Å3/Da / Density % sol: 66.6 % / Description: NONE
Crystal growpH: 6.5
Details: 1.4 M AMMONIUM SULPHATE, 0.1 M BIS TRIS, PH 7.5; 0.1 M LICL

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 19, 2012 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.92→81.44 Å / Num. obs: 287620 / % possible obs: 94.5 % / Observed criterion σ(I): 1.5 / Redundancy: 2.7 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.1
Reflection shellResolution: 1.92→2.02 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.5 / % possible all: 74.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XKR

2xkr


Resolution: 1.93→266.44 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.259 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22975 14356 5.1 %RANDOM
Rwork0.18975 ---
obs0.19177 269594 94.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.564 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å2-0.19 Å2
2--0.11 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.93→266.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18838 0 829 2637 22304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02220427
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1732.03927925
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00852479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35623.26951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.144153282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1615209
X-RAY DIFFRACTIONr_chiral_restr0.1540.23186
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02115417
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.011.512223
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.568219769
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.05738204
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0554.58143
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.928→1.978 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 743 -
Rwork0.35 13804 -
obs--65.41 %
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)
11.6402-0.4556-0.37450.8849-0.21911.37170.0248-0.05190.05230.0680.03650.0718-0.165-0.108-0.06140.14170.0320.08840.01580.01470.0671-18.26220.412-116.4151
20.71680.1196-0.39611.8632-0.18621.37390.040.05180.0862-0.03890.01950.0081-0.1775-0.0882-0.05950.07910.06280.060.05770.05710.0667-51.407135.4767-105.4548
30.6636-0.09880.39351.7816-0.18691.39240.0458-0.0631-0.0850.05750.0140.00830.1704-0.0956-0.05980.0765-0.0691-0.05040.0730.05920.0641-51.429842.818-27.6909
41.7405-0.4520.39160.86330.18051.32770.0236-0.035-0.04470.07320.0339-0.06540.16880.101-0.05740.14540.0388-0.07190.0164-0.02010.0581-28.8718-3.6916.7772
51.40730.54720.02691.0263-0.44881.3110.0145-0.0748-0.03480.04480.04310.07050.0184-0.1852-0.05760.01990.0330.02760.11690.07660.0694-69.4393.9341-71.955
61.4856-0.62110.05661.0984-0.43791.35640.02070.06820.0343-0.04810.03640.0711-0.003-0.1897-0.05720.0221-0.0381-0.02060.13430.07730.0663-69.504774.1093-61.265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 407
2X-RAY DIFFRACTION2B1 - 407
3X-RAY DIFFRACTION3C1 - 407
4X-RAY DIFFRACTION4D1 - 407
5X-RAY DIFFRACTION5E1 - 407
6X-RAY DIFFRACTION6F1 - 407

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