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- PDB-3dl9: Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2 -

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Basic information

Entry
Database: PDB / ID: 3dl9
TitleCrystal structure of CYP2R1 in complex with 1-alpha-hydroxy-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 / 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 / PROTOPORPHYRIN IX CONTAINING FE / Chem-V2H / Vitamin D 25-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.721 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 1-alpha-hydroxy-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
DepositionJun 26, 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.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)114,6478
Polymers110,2832
Non-polymers4,3646
Water2,162120
1
A: Cytochrome P450 2R1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3234
Polymers55,1411
Non-polymers2,1823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 2R1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3234
Polymers55,1411
Non-polymers2,1823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.303, 163.040, 152.588
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

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


Mass: 55141.266 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
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-V2H / (1S,3R,5Z,7E,22E)-9,10-secoergosta-5,7,10,22-tetraene-1,3-diol / 1-alpha-hydroxy-vitamin D2


Mass: 412.648 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H44O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.87 Å3/Da / Density % sol: 68.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 1.2M Ammounium 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 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.72→50 Å / Num. obs: 46055 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.163 / Χ2: 1.99 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.72-2.777.20.95722761.41100
2.77-2.827.40.85722891.35100
2.82-2.877.40.74522811.383100
2.87-2.937.40.63322641.419100
2.93-2.997.40.54622741.453100
2.99-3.067.40.45322791.486100
3.06-3.147.40.3922901.481100
3.14-3.227.40.33522771.554100
3.22-3.327.40.25223081.669100
3.32-3.437.40.21822881.749100
3.43-3.557.30.19322811.89100
3.55-3.697.30.15722802.042100
3.69-3.867.30.13322892.19100
3.86-4.067.20.11823042.371100
4.06-4.327.10.1123102.69100
4.32-4.656.90.09223222.983100
4.65-5.126.90.0923062.939100
5.12-5.866.90.09323402.75100
5.86-7.386.80.08123582.506100
7.38-506.50.04824392.75999.2

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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 3CZH

3czh


Resolution: 2.721→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.192 / WRfactor Rwork: 0.161 / SU B: 10.35 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.402 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Programs coot, prodrg, molprobity have also been used in refinement. 3. THE 2-HYDROXYPROPYL-BETA-CYCLODEXTRIN WAS ADDED TO THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Programs coot, prodrg, molprobity have also been used in refinement. 3. THE 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1369 2.992 %thin shells (sftools)
Rwork0.183 ---
obs0.184 45761 99.213 %-
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: 37.005 Å2
Baniso -1Baniso -2Baniso -3
1-3.837 Å20 Å20 Å2
2---2.163 Å20 Å2
3----1.675 Å2
Refinement stepCycle: LAST / Resolution: 2.721→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7453 0 386 120 7959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228106
X-RAY DIFFRACTIONr_bond_other_d0.0030.025421
X-RAY DIFFRACTIONr_angle_refined_deg1.3922.04811097
X-RAY DIFFRACTIONr_angle_other_deg1.019313168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4625930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27223.47366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.219151218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8411541
X-RAY DIFFRACTIONr_chiral_restr0.0920.21204
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028795
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021696
X-RAY DIFFRACTIONr_nbd_refined0.2110.21860
X-RAY DIFFRACTIONr_nbd_other0.1850.25604
X-RAY DIFFRACTIONr_nbtor_refined0.1860.24055
X-RAY DIFFRACTIONr_nbtor_other0.0880.23844
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.22
X-RAY DIFFRACTIONr_mcbond_it1.33124836
X-RAY DIFFRACTIONr_mcbond_other0.19821867
X-RAY DIFFRACTIONr_mcangle_it2.17137525
X-RAY DIFFRACTIONr_scbond_it1.03523826
X-RAY DIFFRACTIONr_scangle_it1.55533564
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 (%)
2.721-2.79200.2823196335995.147
2.792-2.86700.2653214325798.68
2.867-2.950.2983060.2512848318099.182
2.95-3.040.286340.2463014308198.929
3.04-3.13800.2272989300599.468
3.138-3.2470.2661060.2252781289999.586
3.247-3.3680.2141650.2022639281499.645
3.368-3.50400.1972684268999.814
3.504-3.6570.232300.1862378260999.962
3.657-3.83300.1662471247699.798
3.833-4.03700.1552366237999.454
4.037-4.2770.181770.1482074226599.382
4.277-4.56500.1322114211799.858
4.565-4.9220.1891330.1411857199299.9
4.922-5.37700.15518311831100
5.377-5.9880.201930.17515931686100
5.988-6.8680.265590.191428148999.866
6.868-8.30400.16412841284100
8.304-11.3180.166430.132991103799.711
11.318-300.169230.18664067598.222

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