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- PDB-1equ: TYPE 1 17-BETA HYDROXYSTEROID DEHYDROGENASE EQUILIN COMPLEXED WIT... -

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Basic information

Entry
Database: PDB / ID: 1equ
TitleTYPE 1 17-BETA HYDROXYSTEROID DEHYDROGENASE EQUILIN COMPLEXED WITH NADP+
ComponentsPROTEIN (ESTRADIOL 17 BETA-DEHYDROGENASE 1)
KeywordsOXIDOREDUCTASE / HYDROXYSTEROID DEHYDROGENASE / SHORT CHAIN DEHYDROGENASE / REDUCTASE
Function / homology
Function and homology information


17-beta-hydroxysteroid dehydrogenase (NADP+) activity / 3(or 17)beta-hydroxysteroid dehydrogenase / cellular response to metal ion / estrogen biosynthetic process / estradiol binding / Estrogen biosynthesis / testosterone dehydrogenase (NADP+) activity / testosterone biosynthetic process / : / testosterone dehydrogenase (NAD+) activity ...17-beta-hydroxysteroid dehydrogenase (NADP+) activity / 3(or 17)beta-hydroxysteroid dehydrogenase / cellular response to metal ion / estrogen biosynthetic process / estradiol binding / Estrogen biosynthesis / testosterone dehydrogenase (NADP+) activity / testosterone biosynthetic process / : / testosterone dehydrogenase (NAD+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid biosynthetic process / estrogen metabolic process / NADP+ binding / lysosome organization / small molecule binding / 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 / cytoplasm / cytosol
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
EQUILIN / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSawicki, M.W. / Erman, M. / Puranen, T. / Vihko, P. / Ghosh, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structure of the ternary complex of human 17beta-hydroxysteroid dehydrogenase type 1 with 3-hydroxyestra-1,3,5,7-tetraen-17-one (equilin) and NADP+.
Authors: Sawicki, M.W. / Erman, M. / Puranen, T. / Vihko, P. / Ghosh, D.
History
DepositionDec 2, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: database_PDB_caveat / pdbx_entry_details ...database_PDB_caveat / pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ESTRADIOL 17 BETA-DEHYDROGENASE 1)
B: PROTEIN (ESTRADIOL 17 BETA-DEHYDROGENASE 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5315
Polymers69,7762
Non-polymers1,7553
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-41 kcal/mol
Surface area21680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.020, 114.160, 114.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

NCS oper: (Code: given
Matrix: (0.96803, 0.240107, -0.072577), (0.240103, -0.970707, -0.008915), (-0.072592, -0.008796, -0.997323)
Vector: -0.496, 22.8112, 61.8604)

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Components

#1: Protein PROTEIN (ESTRADIOL 17 BETA-DEHYDROGENASE 1)


Mass: 34887.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P14061, 17beta-estradiol 17-dehydrogenase
#2: 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
#3: Chemical ChemComp-EQI / EQUILIN


Mass: 268.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growpH: 7.5
Details: VAP. DIFF. FROM 28% PEG 4000 IN HEPES BUFFER, PH 7.5, CONTAINING 1 MM EQUILIN, pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
128 %PEG40001reservoir
31 mMequilin1reservoir
2HEPES1reservoir

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 26, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→99 Å / Num. obs: 11408 / % possible obs: 93.1 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 6.5
Reflection shellResolution: 3→3.23 Å / Mean I/σ(I) obs: 1.7 / % possible all: 92
Reflection
*PLUS
Num. measured all: 28469
Reflection shell
*PLUS
% possible obs: 92 % / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BHS

1bhs


Resolution: 3→12 Å / Rfactor Rfree error: 0.03 / Cross valid method: THROUGHOUT / σ(F): 1
Details: THE EXTENDED LOOP REGION OF THE B SUBUNIT (186-200) WAS MODELED AFTER THE APO STRUCTURE EXTENDED LOOP
RfactorNum. reflection% reflectionSelection details
Rfree0.315 494 5 %RANDOM
Rwork0.182 ---
obs0.182 9322 93.1 %-
Refinement stepCycle: LAST / Resolution: 3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 116 18 4492
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.65
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.06
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.61
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11RESTRAINTSX-RAY DIFFRACTION3.5100
22X-RAY DIFFRACTION3.510
33X-RAY DIFFRACTION3.55
LS refinement shellResolution: 3→3.23 Å / Rfactor Rfree: 0.373 / Rfactor Rwork: 0.223 / Total num. of bins used: 8
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.06
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.61

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