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- PDB-3czh: Crystal structure of CYP2R1 in complex with vitamin D2 -

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Basic information

Entry
Database: PDB / ID: 3czh
TitleCrystal structure of CYP2R1 in complex with vitamin D2
ComponentsCytochrome P450 2R1
KeywordsOXIDOREDUCTASE / cytochrome p450 / vitamin d / vitamin s 25-hydroxylase / drug metabolism / Structural Genomics / Structural Genomics Consortium / SGC / Disease mutation / Endoplasmic reticulum / Heme / Iron / Membrane / Metal-binding / Microsome / Monooxygenase
Function / homology
Function and homology information


vitamin D 25-hydroxylase / vitamin metabolic process / response to cesium ion / calcitriol biosynthetic process from calciol / D3 vitamins binding / Vitamins / Defective CYP27B1 causes VDDR1B / organic acid metabolic process / vitamin D3 25-hydroxylase activity / Vitamin D (calciferol) metabolism ...vitamin D 25-hydroxylase / vitamin metabolic process / response to cesium ion / calcitriol biosynthetic process from calciol / D3 vitamins binding / Vitamins / Defective CYP27B1 causes VDDR1B / organic acid metabolic process / vitamin D3 25-hydroxylase activity / Vitamin D (calciferol) metabolism / vitamin D metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / response to ionizing radiation / steroid hydroxylase activity / xenobiotic metabolic process / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / protein homodimerization activity / cytoplasm
Similarity search - Function
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
beta-cyclodextrin / Chem-D2V / PROTOPORPHYRIN IX CONTAINING FE / Vitamin D 25-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.3 Å
AuthorsStrushkevich, N.V. / Tempel, W. / Gilep, A.A. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Wilkstrom, M. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of CYP2R1 in complex with vitamin D2.
Authors: Strushkevich, N.V. / Tempel, W. / Gilep, A.A. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Wilkstrom, M. / Bochkarev, A. / Park, H.
History
DepositionApr 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_alt_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 / _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.pdbx_number_of_molecules / _entity.type / _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 / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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: Cytochrome P450 2R1
B: Cytochrome P450 2R1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,16729
Polymers110,8352
Non-polymers4,33227
Water2,594144
1
A: Cytochrome P450 2R1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,58414
Polymers55,4181
Non-polymers2,16613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 2R1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,58415
Polymers55,4181
Non-polymers2,16614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.361, 163.393, 152.289
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Cytochrome P450 2R1 / Vitamin D 25-hydroxylase


Mass: 55417.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2R1 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q6VVX0, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one ...References: UniProt: Q6VVX0, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor
#2: Polysaccharide Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 2
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, 169 molecules

#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 21 / Source method: obtained synthetically
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-D2V / (3S,5Z,7E,22E)-9,10-secoergosta-5,7,10,22-tetraen-3-ol / Vitamin D2 / Ergocalciferol / Deltalin


Mass: 396.648 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H44O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.85 Å3/Da / Density % sol: 68.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 1.2M Ammonium sulfate, 0.1M ADA, pH 6.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 73584 / % possible obs: 97.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.099 / Χ2: 1.811 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.344.80.63631561.59984.7
2.34-2.385.40.59333891.61290.5
2.38-2.435.90.57733891.77191.5
2.43-2.486.10.55235141.63293.4
2.48-2.536.20.49936131.53695.9
2.53-2.596.50.49136231.46497.4
2.59-2.666.80.45637071.52299.4
2.66-2.737.10.41637551.43899.9
2.73-2.817.30.36837771.378100
2.81-2.97.40.30237051.423100
2.9-37.40.24237491.465100
3-3.127.40.18737841.54100
3.12-3.267.40.14637431.705100
3.26-3.447.30.10637891.84599.9
3.44-3.657.30.08337451.963100
3.65-3.937.20.06537952.172100
3.93-4.337.10.05537882.429100
4.33-4.956.90.0538102.808100
4.95-6.246.70.04838572.592100
6.24-506.60.03138962.07497.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.3.0037refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-3000data reduction
REFMAC5.3.0037phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3C6G

3c6g


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.209 / WRfactor Rwork: 0.187 / SU B: 5.883 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2-HYDROXYPROPYL-BETA-CYCLODEXTRIN WAS ADDED TO THE PROTEIN SAMPLE. DUE TO LIMITED RESOLUTION OF THE ELECTRON DENSITY MAP AND LACK OF A ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2-HYDROXYPROPYL-BETA-CYCLODEXTRIN WAS ADDED TO THE PROTEIN SAMPLE. DUE TO LIMITED RESOLUTION OF THE ELECTRON DENSITY MAP AND LACK OF A PRECISE CHEMICAL DESCRIPTION OF THE ADDITIVE, IT WAS MODELED HERE AS BETA-CYCLODEXTRIN. 3. Programs coot, molprobity, sftools, prodrg have also been used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2215 3.019 %thin shells
Rwork0.205 ---
obs0.206 73363 96.673 %-
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 mean: 37.917 Å2
Baniso -1Baniso -2Baniso -3
1-3.72 Å20 Å20 Å2
2---2.344 Å20 Å2
3----1.376 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7444 0 405 144 7993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228095
X-RAY DIFFRACTIONr_bond_other_d0.0020.025414
X-RAY DIFFRACTIONr_angle_refined_deg1.2732.04611082
X-RAY DIFFRACTIONr_angle_other_deg1.0563.00113066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3815930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1323.379364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.308151212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5981542
X-RAY DIFFRACTIONr_chiral_restr0.0860.21202
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028784
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021684
X-RAY DIFFRACTIONr_nbd_refined0.1960.21677
X-RAY DIFFRACTIONr_nbd_other0.1840.25363
X-RAY DIFFRACTIONr_nbtor_refined0.180.23955
X-RAY DIFFRACTIONr_nbtor_other0.0880.23793
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.010.21
X-RAY DIFFRACTIONr_mcbond_it1.45824777
X-RAY DIFFRACTIONr_mcbond_other0.27721867
X-RAY DIFFRACTIONr_mcangle_it2.33737519
X-RAY DIFFRACTIONr_scbond_it1.22823823
X-RAY DIFFRACTIONr_scangle_it1.81733555
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 (%)
2.3-2.36100.2744220551676.505
2.361-2.42500.2694920540091.111
2.425-2.4950.3014260.274455524793.025
2.495-2.57100.2574885507596.256
2.571-2.65500.2614916496499.033
2.655-2.7470.324180.2554351478399.707
2.747-2.8500.2414623463099.849
2.85-2.9650.2753410.2394124447199.866
2.965-3.09500.2294268427099.953
3.095-3.2450.227340.2254082411899.951
3.245-3.4180.2192400.2073660390199.974
3.418-3.6230.2131030.23613372099.892
3.623-3.8690.2351270.1743356348499.971
3.869-4.1730.1841770.1723081326999.664
4.173-4.56200.1543016302099.868
4.562-5.0860.211330.1662621276099.783
5.086-5.8450.201930.1942344243899.959
5.845-7.0920.278590.2142043210399.952
7.092-9.760.161430.1741622167399.522
9.76-300.156210.177948104692.639

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