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- PDB-3v8d: Crystal structure of human CYP7A1 in complex with 7-ketocholesterol -

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Basic information

Entry
Database: PDB / ID: 3v8d
TitleCrystal structure of human CYP7A1 in complex with 7-ketocholesterol
ComponentsCholesterol 7-alpha-monooxygenase
KeywordsOXIDOREDUCTASE / cytochrome / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cholesterol 7alpha-monooxygenase / 24-hydroxycholesterol 7alpha-hydroxylase / cholesterol 7-alpha-monooxygenase activity / 24-hydroxycholesterol 7alpha-hydroxylase activity / negative regulation of collagen biosynthetic process / bile acid biosynthetic process / sterol metabolic process / cellular response to cholesterol / negative regulation of fatty acid biosynthetic process / regulation of bile acid biosynthetic process ...cholesterol 7alpha-monooxygenase / 24-hydroxycholesterol 7alpha-hydroxylase / cholesterol 7-alpha-monooxygenase activity / 24-hydroxycholesterol 7alpha-hydroxylase activity / negative regulation of collagen biosynthetic process / bile acid biosynthetic process / sterol metabolic process / cellular response to cholesterol / negative regulation of fatty acid biosynthetic process / regulation of bile acid biosynthetic process / positive regulation of cholesterol biosynthetic process / cholesterol catabolic process / bile acid and bile salt transport / bile acid signaling pathway / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / cholesterol homeostasis / cellular response to glucose stimulus / PPARA activates gene expression / response to ethanol / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane
Similarity search - Function
Cholesterol 7-alpha-monooxygenase / Cytochrome P450, cholesterol 7-alpha-monooxygenase-type / Cytochrome P450, E-class, group IV / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 ...Cholesterol 7-alpha-monooxygenase / Cytochrome P450, cholesterol 7-alpha-monooxygenase-type / Cytochrome P450, E-class, group IV / 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
(3beta,8alpha,9beta)-3-hydroxycholest-5-en-7-one / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 7A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsStrushkevich, N. / Tempel, W. / MacKenzie, F. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Usanov, S.A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human CYP7A1 in complex with 7-ketocholesterol
Authors: Strushkevich, N. / Tempel, W. / MacKenzie, F. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Usanov, S.A. / Park, H.
History
DepositionDec 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 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_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_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.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_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_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_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

Downloads & links

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Assembly

Deposited unit
A: Cholesterol 7-alpha-monooxygenase
B: Cholesterol 7-alpha-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,57426
Polymers112,9642
Non-polymers2,61124
Water6,377354
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-161 kcal/mol
Surface area36670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.618, 74.220, 87.933
Angle α, β, γ (deg.)66.330, 75.530, 69.620
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cholesterol 7-alpha-monooxygenase / CYPVII / Cholesterol 7-alpha-hydroxylase / Cytochrome P450 7A1


Mass: 56481.836 Da / Num. of mol.: 2 / Fragment: UNP residues 25-503 / Mutation: T104L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP7A1, CYP7 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P22680, EC: 1.14.13.17

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Non-polymers , 5 types, 378 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-0GV / (3beta,8alpha,9beta)-3-hydroxycholest-5-en-7-one / 7-ketocholesterol


Mass: 400.637 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H44O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 14 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.8 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 291 K / pH: 5.6
Details: 30% PEG-400, 0.2M lithium sulfate, 0.1M trisodium citrate, pH 5.6, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 92430 / % possible obs: 97.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.074 / Χ2: 1.35 / Net I/σ(I): 9.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.973.70.84890891.046196.4
1.97-2.053.70.62691881.057196.7
2.05-2.143.70.41191961.112196.9
2.14-2.253.70.28691701.145197
2.25-2.393.80.21192141.2197.4
2.39-2.583.90.16292371.264197.7
2.58-2.843.90.1193241.341198.1
2.84-3.253.90.07293281.629198.4
3.25-4.093.90.04192921.734198.4
4.09-503.90.03593921.86199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3DAX

3dax


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.173 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.55 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY Geometry restraints for 7-ketocholesterol wer prepared by the PRODRG server. Heme geometry restraints were ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY Geometry restraints for 7-ketocholesterol wer prepared by the PRODRG server. Heme geometry restraints were modified from the CCP4 default using data from the Cambridge Structural Database, using the Mogul query tool. PHENIX, COOT and the MOLPROBITY server were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2066 2.241 %THIN SHELLS (SFTOOLS)
Rwork0.1852 ---
obs0.186 92179 97.601 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 89.28 Å2 / Biso mean: 26.151 Å2 / Biso min: 15.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.613 Å2-0.549 Å2-0.243 Å2
2--0.26 Å20.72 Å2
3---0.279 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7479 0 188 354 8021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.027981
X-RAY DIFFRACTIONr_bond_other_d0.0030.025375
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.98310886
X-RAY DIFFRACTIONr_angle_other_deg0.8083.00413103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4085984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51823.585357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.886151308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4591546
X-RAY DIFFRACTIONr_chiral_restr0.0610.21202
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218833
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021693
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.94900.2876751701396.264
1.949-2.00300.2676555678496.624
2.003-2.0610.2724000.256036665096.782
2.061-2.12400.2336199639696.92
2.124-2.19300.2156014620696.906
2.193-2.270.2563660.2085446598597.109
2.27-2.35600.1975679583797.293
2.356-2.4520.2412900.25173559497.658
2.452-2.5600.1995260538397.715
2.56-2.6850.2552540.1944759511198.083
2.685-2.8300.1934785487598.154
2.83-3.0010.2152060.1864296457898.34
3.001-3.20700.1854283435398.392
3.207-3.4630.2161510.173841405198.544
3.463-3.7920.2281470.1593489369398.457
3.792-4.23600.1443319337098.487
4.236-4.8860.182850.1392840296598.651
4.886-5.970.192760.1662411250299.4
5.97-8.3830.199770.1941862194899.538
8.383-500.271140.1751068109698.723

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