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- PDB-1fdv: HUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 MUTANT H221L CO... -

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Basic information

Entry
Database: PDB / ID: 1fdv
TitleHUMAN 17-BETA-HYDROXYSTEROID-DEHYDROGENASE TYPE 1 MUTANT H221L COMPLEXED WITH NAD+
Components17-BETA-HYDROXYSTEROID DEHYDROGENASE
KeywordsDEHYDROGENASE / 17-BETA-HYDROXYSTEROID / MUTANT / NAD
Function / homology
Function and homology information


estradiol binding / 3(or 17)beta-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)] activity / cellular response to metal ion / Estrogen biosynthesis / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone dehydrogenase (NAD+) activity / testosterone biosynthetic process ...estradiol binding / 3(or 17)beta-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)] activity / cellular response to metal ion / Estrogen biosynthesis / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone dehydrogenase (NAD+) activity / testosterone biosynthetic process / 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 / lysosome organization / The canonical retinoid cycle in rods (twilight vision) / small molecule binding / adipose tissue development / catalytic activity / skeletal muscle tissue development / steroid binding / bone development / gene expression / NADP binding / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 17-beta-hydroxysteroid dehydrogenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 15, 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: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Nov 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 1.6Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 17-BETA-HYDROXYSTEROID DEHYDROGENASE
B: 17-BETA-HYDROXYSTEROID DEHYDROGENASE
C: 17-BETA-HYDROXYSTEROID DEHYDROGENASE
D: 17-BETA-HYDROXYSTEROID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,83412
Polymers139,7964
Non-polymers3,0388
Water90150
1
A: 17-BETA-HYDROXYSTEROID DEHYDROGENASE
B: 17-BETA-HYDROXYSTEROID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4176
Polymers69,8982
Non-polymers1,5194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-85 kcal/mol
Surface area21680 Å2
MethodPISA
2
C: 17-BETA-HYDROXYSTEROID DEHYDROGENASE
D: 17-BETA-HYDROXYSTEROID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4176
Polymers69,8982
Non-polymers1,5194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-85 kcal/mol
Surface area21760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.120, 79.110, 120.470
Angle α, β, γ (deg.)90.00, 91.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.998368, -0.048502, -0.030139), (-0.026832, -0.067439, 0.997363), (-0.050406, 0.996544, 0.066027)70.16706, -48.69884, 48.11555
2given(-0.010301, -0.002726, -0.999943), (-0.012773, -0.999914, 0.002857), (-0.999865, 0.012802, 0.010265)55.69549, 48.118, 59.67365
3given(0.040503, 0.049034, 0.997976), (-0.996359, 0.076977, 0.036655), (-0.075024, -0.995826, 0.051973)10.51629, 6.21388, 97.25399

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Components

#1: Protein
17-BETA-HYDROXYSTEROID DEHYDROGENASE


Mass: 34948.961 Da / Num. of mol.: 4 / Mutation: H221L
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.96 Å3/Da / Density % sol: 69 %
Crystal growpH: 6.3
Details: PROTEIN WAS CRYSTALLIZED FROM 2 M AMMONIUM SULFATE, 100 MM SODIUM PHOSPHATE BUFFER PH 6.3, 1 MM NAD+, 100 MM NACL; THEN SOAKED IN 27 % GLYCEROL, 2.3 M AMMONIUM SULFATE, 100 MM SODIUM ...Details: PROTEIN WAS CRYSTALLIZED FROM 2 M AMMONIUM SULFATE, 100 MM SODIUM PHOSPHATE BUFFER PH 6.3, 1 MM NAD+, 100 MM NACL; THEN SOAKED IN 27 % GLYCEROL, 2.3 M AMMONIUM SULFATE, 100 MM SODIUM PHOSPHATE BUFFER PH 6.1, 80 MM NACL, 1 MM NAD+
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlenzyme11
21 mMEDTA11
30.2 mMdithiothreitol11
420 %glycerol11
52 mMbeta-octylglucoside11
6100 mMHEPES12
7100 mM12MgCl2
80.5 mME212
92-4 %propanediol12
1030 %PEG400012

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.9795
DetectorType: ESRF / Detector: CCD / Date: Nov 1, 1995 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 56921 / % possible obs: 91.6 % / Observed criterion σ(I): 0 / Redundancy: 3.61 % / Rsym value: 0.146
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 3.94 % / Rsym value: 0.418 / % possible all: 98.5
Reflection
*PLUS
Rmerge(I) obs: 0.146
Reflection shell
*PLUS
% possible obs: 98.5 % / Rmerge(I) obs: 0.418

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Processing

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

1fdt


Resolution: 3.1→10 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1594 5 %RANDOM
Rwork0.219 ---
obs-30594 83 %-
Displacement parametersBiso mean: 25.33 Å2
Refinement stepCycle: LAST / Resolution: 3.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8568 0 176 70 8814
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0430.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0590.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.2460.2
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: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS

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