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- PDB-3km0: 17betaHSD1 in complex with 3beta-diol -

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Basic information

Entry
Database: PDB / ID: 3km0
Title17betaHSD1 in complex with 3beta-diol
ComponentsEstradiol 17-beta-dehydrogenase 1
KeywordsOXIDOREDUCTASE / Lipid synthesis / Steroid biosynthesis
Function / homology
Function and homology information


17-beta-hydroxysteroid dehydrogenase (NADP+) activity / 3(or 17)beta-hydroxysteroid dehydrogenase / estradiol binding / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / : / testosterone biosynthetic process / testosterone dehydrogenase (NAD+) activity ...17-beta-hydroxysteroid dehydrogenase (NADP+) activity / 3(or 17)beta-hydroxysteroid dehydrogenase / estradiol binding / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / : / testosterone biosynthetic process / testosterone dehydrogenase (NAD+) activity / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid biosynthetic process / estrogen metabolic process / NADP+ binding / small molecule binding / lysosome organization / The canonical retinoid cycle in rods (twilight vision) / catalytic activity / adipose tissue development / skeletal muscle tissue development / steroid binding / bone development / NADP binding / gene expression / protein homodimerization activity / cytosol / cytoplasm
Similarity search - Function
17beta-dehydrogenase / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-ALPHA-ANDROSTANE-3-BETA,17BETA-DIOL / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsMazumdar, M. / Lin, S.-X.
CitationJournal: To be Published
Title: Molecular basis of sex-steroid translation
Authors: Mazumdar, M. / Chen, J. / Lin, S.-X.
History
DepositionNov 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Mar 13, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_distant_solvent_atoms ...atom_site / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Estradiol 17-beta-dehydrogenase 1
B: Estradiol 17-beta-dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8476
Polymers69,7762
Non-polymers2,0724
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8900 Å2
ΔGint-42 kcal/mol
Surface area21330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.420, 43.120, 121.100
Angle α, β, γ (deg.)90.00, 128.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Estradiol 17-beta-dehydrogenase 1 / 17-beta-hydroxysteroid dehydrogenase type 1 / 17-beta-HSD 1 / Placental 17-beta-hydroxysteroid ...17-beta-hydroxysteroid dehydrogenase type 1 / 17-beta-HSD 1 / Placental 17-beta-hydroxysteroid dehydrogenase / 20 alpha-hydroxysteroid dehydrogenase / 20-alpha-HSD / E2DH


Mass: 34887.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: protein purified from human placenta / Source: (natural) Homo sapiens (human)
References: UniProt: P14061, 17beta-estradiol 17-dehydrogenase
#2: Chemical ChemComp-AOM / 5-ALPHA-ANDROSTANE-3-BETA,17BETA-DIOL


Mass: 292.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H32O2 / Comment: hormone*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→18.98 Å / Num. all: 24446 / Num. obs: 25734

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Processing

Software
NameVersionClassification
CrystalCleardata collection
XDSdata scaling
REFMAC5.2.0005refinement
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→18.98 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.871 / SU B: 9.941 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.413 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31178 1286 5 %RANDOM
Rwork0.23304 ---
obs0.23695 24446 100 %-
all-25734 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.894 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→18.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4212 0 138 194 4544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0390.0224337
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.2781.9965896
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6715546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47622.179179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.86515712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2011544
X-RAY DIFFRACTIONr_chiral_restr0.2250.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023212
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3070.22055
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3340.22842
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2164
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3480.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6381.52887
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.55524384
X-RAY DIFFRACTIONr_scbond_it4.35931717
X-RAY DIFFRACTIONr_scangle_it6.0394.51512
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 95 -
Rwork0.261 1811 -
obs--100 %

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