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- PDB-3mzs: Crystal Structure of Cytochrome P450 CYP11A1 in complex with 22-h... -

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Basic information

Entry
Database: PDB / ID: 3mzs
TitleCrystal Structure of Cytochrome P450 CYP11A1 in complex with 22-hydroxy-cholesterol
ComponentsCholesterol side-chain cleavage enzyme
KeywordsOXIDOREDUCTASE / CYP11A1 / CYTOCHROME P450 / MONOOXYGENASE / SIDE CHAIN CLEAVAGE ENZYME / CHOLESTEROL / Cholesterol 20-22-desmolase / STEROID METABOLISM / HEME
Function / homology
Function and homology information


cholesterol monooxygenase (side-chain-cleaving) / cholesterol monooxygenase (side-chain-cleaving) activity / vitamin D metabolic process / C21-steroid hormone biosynthetic process / cholesterol metabolic process / mitochondrial inner membrane / iron ion binding / heme binding / mitochondrion
Similarity search - Function
Cholesterol side-chain cleavage enzyme, mitochondrial / Cytochrome P450, E-class, group I / 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
(3alpha,8alpha,22R)-cholest-5-ene-3,22-diol / PROTOPORPHYRIN IX CONTAINING FE / ISOPROPYL ALCOHOL / Cholesterol side-chain cleavage enzyme, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsStout, C.D. / Annalora, A. / Mast, N. / Pikuleva, I.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Basis for Three-step Sequential Catalysis by the Cholesterol Side Chain Cleavage Enzyme CYP11A1.
Authors: Mast, N. / Annalora, A.J. / Lodowski, D.T. / Palczewski, K. / Stout, C.D. / Pikuleva, I.A.
History
DepositionMay 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ref_seq_dif.details / _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: Cholesterol side-chain cleavage enzyme
B: Cholesterol side-chain cleavage enzyme
C: Cholesterol side-chain cleavage enzyme
D: Cholesterol side-chain cleavage enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,78416
Polymers228,4674
Non-polymers4,31712
Water1,65792
1
A: Cholesterol side-chain cleavage enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1964
Polymers57,1171
Non-polymers1,0793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cholesterol side-chain cleavage enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1964
Polymers57,1171
Non-polymers1,0793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cholesterol side-chain cleavage enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1964
Polymers57,1171
Non-polymers1,0793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cholesterol side-chain cleavage enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1964
Polymers57,1171
Non-polymers1,0793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.450, 94.630, 113.500
Angle α, β, γ (deg.)90.000, 89.960, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13D
23A

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: IPA / End label comp-ID: IPA / Refine code: 6 / Auth seq-ID: 6 - 502 / Label seq-ID: 6

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11BB - J
21AA - G
12CC - M
22AA - G
13DD - P
23AA - G

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Cholesterol side-chain cleavage enzyme / Cytochrome P450 11A1 / CYPXIA1 / Cytochrome P450(scc) / Cholesterol desmolase


Mass: 57116.816 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CYP11A1 / Plasmid: PUC18 / Production host: Escherichia coli (E. coli)
References: UniProt: P00189, cholesterol monooxygenase (side-chain-cleaving)
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-HC9 / (3alpha,8alpha,22R)-cholest-5-ene-3,22-diol


Mass: 402.653 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O2
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 285 K / Method: vapor diffusion / pH: 7
Details: 16% PEG 1000, 10% Jeffamine ED-2001, 20% glycerol, 0.1 M MES, pH 7.0, VAPOR DIFFUSION, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 22, 2010 / Details: Rh coated flat mirror
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.546
11-h,-k,l20.454
ReflectionResolution: 2.5→113.5 Å / Num. all: 76291 / Num. obs: 76291 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 74.2 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 5.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 1.6 / Num. unique all: 11367 / Rsym value: 0.444 / % possible all: 97.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASERphasing
DMphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3K9V

3k9v


Resolution: 2.5→60.01 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.321 / WRfactor Rwork: 0.305 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.603 / SU B: 16.405 / SU ML: 0.338 / SU R Cruickshank DPI: 0.201 / SU Rfree: 0.072 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Non-crystallographic symmetry: the crystal is pseudo-orthorhombic (P212121) with true symmetry P21 with 4 molecules in the asymmetric unit. The crystal exhibits partial merohedral twinning ...Details: Non-crystallographic symmetry: the crystal is pseudo-orthorhombic (P212121) with true symmetry P21 with 4 molecules in the asymmetric unit. The crystal exhibits partial merohedral twinning with twin law h,k,l; -h,-k,l and twin fractions 0.546, 0.453. RAMACHANDRAN OUTLIERS: BASED ON REFERENCE LOVELL, DAVIS, ET AL., PROTEINS 50: 437-450 (2003) AND CALCULATION BY MOLPROBITY, THERE ARE 41 RAMACHANDRAN OUTLIERS; 97.8% RESIDUES ARE IN ALLOWED REGIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 3812 5 %RANDOM
Rwork0.266 ---
obs0.266 72447 94.9 %-
all-76259 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 99.19 Å2 / Biso mean: 65.893 Å2 / Biso min: 18.65 Å2
Baniso -1Baniso -2Baniso -3
1--66.06 Å20 Å2-11.86 Å2
2--9.17 Å20 Å2
3---56.89 Å2
Refinement stepCycle: LAST / Resolution: 2.5→60.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15616 0 304 92 16012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02118268
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.9528000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7117.53752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.7323.265784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.5152852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.32715116
X-RAY DIFFRACTIONr_chiral_restr0.1490.22364
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02120204
X-RAY DIFFRACTIONr_mcbond_it0.981.59416
X-RAY DIFFRACTIONr_mcangle_it1.788215332
X-RAY DIFFRACTIONr_scbond_it2.51136976
X-RAY DIFFRACTIONr_scangle_it3.9534.56928
Refine LS restraints NCS

Dom-ID: 1 / Number: 3980 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDTypeRms dev position (Å)Weight position
1BLOOSE POSITIONAL0.495
1BLOOSE THERMAL2.6810
2CLOOSE POSITIONAL0.475
2CLOOSE THERMAL2.2110
3DLOOSE POSITIONAL0.485
3DLOOSE THERMAL2.7310
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 334 -
Rwork0.423 5446 -
all-5780 -
obs-5446 97.54 %

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