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- PDB-1fdw: HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 MUTANT H221Q CO... -

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Basic information

Entry
Database: PDB / ID: 1fdw
TitleHUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 MUTANT H221Q COMPLEXED WITH ESTRADIOL
Components17-BETA-HYDROXYSTEROID DEHYDROGENASE
KeywordsDEHYDROGENASE / 17-BETA-HYDROXYSTEROID / MUTANT / ESTRADIOL / NADP
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 / NADP+ binding / estrogen metabolic process / 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 / 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
ESTRADIOL / 17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMazza, C. / Breton, R. / Housset, D. / Fontecilla-Camps, J.-C.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: Unusual charge stabilization of NADP+ in 17beta-hydroxysteroid dehydrogenase.
Authors: Mazza, C. / Breton, R. / Housset, D. / Fontecilla-Camps, J.C.
#1: Journal: Thesis, Universite Joseph Fourier / Year: 1997
Title: Human Type I 17Beta-Hydroxysteroid Dehydrogenase: Site Directed Mutagenesis and X-Ray Crystallography Structure-Function Analysis
Authors: Mazza, C.
#2: Journal: Structure / Year: 1996
Title: The Structure of a Complex of Human 17Beta-Hydroxysteroid Dehydrogenase with Estradiol and Nadp+ Identifies Two Principal Targets for the Design of Inhibitors
Authors: Breton, R. / Housset, D. / Mazza, C. / Fontecilla-Camps, J.C.
#3: Journal: Structure / Year: 1995
Title: Structure of Human Estrogenic 17 Beta-Hydroxysteroid Dehydrogenase at 2.20 A Resolution
Authors: Ghosh, D. / Pletnev, V.Z. / Zhu, D.W. / Wawrzak, Z. / Duax, W.L. / Pangborn, W. / Labrie, F. / Lin, S.X.
History
DepositionJan 16, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 17-BETA-HYDROXYSTEROID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2362
Polymers34,9641
Non-polymers2721
Water1448
1
A: 17-BETA-HYDROXYSTEROID DEHYDROGENASE
hetero molecules

A: 17-BETA-HYDROXYSTEROID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4734
Polymers69,9282
Non-polymers5452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6510 Å2
ΔGint-39 kcal/mol
Surface area22680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.670, 45.490, 61.630
Angle α, β, γ (deg.)90.00, 98.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 17-BETA-HYDROXYSTEROID DEHYDROGENASE


Mass: 34963.930 Da / Num. of mol.: 1 / Mutation: H221Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Plasmid: PVL1393 / Cellular location (production host): CYTOPLASM / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P14061, 17beta-estradiol 17-dehydrogenase
#2: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM PEG 4000 30%, 100 MM HEPES BUFFER PH 7.0, 100 MM MGCL2, 0.5 MM ESTRADIOL, PROPANE DIOL 2-4%
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlenzyme11
21 mMEDTA11
30.2 mMdithiothreitol11
420 %glycerol11
52 mMbeta-octylglucoside11
6100 mMsodium phosphate12
71 mMNAD(P)+12
8100 mM12NaCl
92.2-4.4 mMdecyl-beta-D-maltoside12or 9-18mM octyl-beta-D-thioglucopyranoside
102-2.4 Mammonium sulfate12

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Apr 1, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→35.8 Å / Num. obs: 6352 / % possible obs: 65.2 % / Observed criterion σ(I): 0 / Redundancy: 2.54 % / Rsym value: 0.071
Reflection shellResolution: 2.7→2.83 Å
Reflection
*PLUS
Rmerge(I) obs: 0.071

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
XENGENdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FDT

1fdt


Resolution: 2.7→10 Å / σ(F): 2
Details: THE LOOP 191 - 197 HAS BEEN EXCLUDED FROM THE COORDINATE FILE.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 229 5 %RANDOM
Rwork0.178 ---
obs-4887 --
Displacement parametersBiso mean: 16.29 Å2
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2128 0 20 8 2156
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0310.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.4170.5
X-RAY DIFFRACTIONp_mcangle_it0.7681
X-RAY DIFFRACTIONp_scbond_it0.6840.5
X-RAY DIFFRACTIONp_scangle_it1.141
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.1780.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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