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- PDB-4apy: Ethylene glycol-bound form of P450 CYP125A3 from Mycobacterium sm... -

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Basic information

Entry
Database: PDB / ID: 4apy
TitleEthylene glycol-bound form of P450 CYP125A3 from Mycobacterium smegmatis
ComponentsP450 HEME-THIOLATE PROTEIN
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 / 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 / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFrank, D.J. / Garcia Fernandez, E. / Kells, P.M. / Garcia Lopez, J.L. / Podust, L.M. / 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
DepositionApr 9, 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 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)49,32114
Polymers47,9871
Non-polymers1,33513
Water6,107339
1
A: P450 HEME-THIOLATE PROTEIN
hetero molecules

A: P450 HEME-THIOLATE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,64328
Polymers95,9742
Non-polymers2,66926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area9080 Å2
ΔGint-40.2 kcal/mol
Surface area32040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.188, 108.188, 120.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-1426-

CL

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Components

#1: Protein P450 HEME-THIOLATE PROTEIN / CYP125A3


Mass: 47986.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Plasmid: PCW / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: A0R4Y3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details1,2-ETHANEDIOL (EDO): CRYO-PROTECTANT AGENT PROTOPORPHYRIN IX CONTAINING FE (HEM): HEME THIOLATE ...1,2-ETHANEDIOL (EDO): CRYO-PROTECTANT AGENT PROTOPORPHYRIN IX CONTAINING FE (HEM): HEME THIOLATE BOND TO CYS 360
Sequence details6XHIS TAG IS 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: 3.86 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growpH: 6.5
Details: 45% TACSIMATE, PH 7.0; 2% GLUCOSE; 0.1 M NA CACODYLATE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 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: 2→80.32 Å / Num. obs: 46604 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 4.7 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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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 2X5W

2x5w


Resolution: 2→76.5 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.364 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20553 2341 5.1 %RANDOM
Rwork0.16405 ---
obs0.16604 43952 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.835 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2→76.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 0 88 339 3639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0223421
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0561.9964645
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.275425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45124.472161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52115546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9381524
X-RAY DIFFRACTIONr_chiral_restr0.1470.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212654
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_it1.21.52099
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.13823384
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.44131322
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2484.51261
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: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 172 -
Rwork0.307 3176 -
obs--97.95 %

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