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- PDB-4fj1: Crystal Structure of the ternary complex between a fungal 17beta-... -

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Basic information

Entry
Database: PDB / ID: 4fj1
TitleCrystal Structure of the ternary complex between a fungal 17beta-hydroxysteroid dehydrogenase (Holo form) and genistein
Components17beta-hydroxysteroid dehydrogenase
Keywordsoxidoreductase/Oxidoreductase inhibitor / Short chain Dehydrogenase/Reductase / Rossmann Fold / Oxidoreductase / NADP(H) / oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


organic substance biosynthetic process / cellular biosynthetic process / oxidoreductase activity, acting on CH-OH group of donors / nucleotide binding
Similarity search - Function
PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / 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
GENISTEIN / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 17beta-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesCochliobolus lunatus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCassetta, A. / Lamba, D. / Krastanova, I.
CitationJournal: J. Steroid Biochem. Mol. Biol. / Year: 2017
Title: Structural basis for inhibition of 17 beta-hydroxysteroid dehydrogenases by phytoestrogens: The case of fungal 17 beta-HSDcl.
Authors: Cassetta, A. / Stojan, J. / Krastanova, I. / Kristan, K. / Brunskole Svegelj, M. / Lamba, D. / Rizner, T.L.
History
DepositionJun 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Structure summary
Revision 1.2Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Sep 13, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 17beta-hydroxysteroid dehydrogenase
B: 17beta-hydroxysteroid dehydrogenase
C: 17beta-hydroxysteroid dehydrogenase
D: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,19822
Polymers115,7464
Non-polymers4,45218
Water5,981332
1
A: 17beta-hydroxysteroid dehydrogenase
B: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,02110
Polymers57,8732
Non-polymers2,1488
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-16 kcal/mol
Surface area19440 Å2
MethodPISA
2
C: 17beta-hydroxysteroid dehydrogenase
D: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,17712
Polymers57,8732
Non-polymers2,30410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-9 kcal/mol
Surface area19400 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23900 Å2
ΔGint-64 kcal/mol
Surface area31700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.370, 113.890, 69.400
Angle α, β, γ (deg.)90.00, 102.73, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEAA12 - 26912 - 269
21ILEILEBB12 - 26912 - 269
12PROPROAA13 - 26913 - 269
22PROPROCC13 - 26913 - 269
13THRTHRAA10 - 27010 - 270
23THRTHRDD10 - 27010 - 270
14PROPROBB13 - 26913 - 269
24PROPROCC13 - 26913 - 269
15ILEILEBB12 - 26912 - 269
25ILEILEDD12 - 26912 - 269
16PROPROCC13 - 26913 - 269
26PROPRODD13 - 26913 - 269

NCS ensembles :
ID
1
2
3
4
5
6
DetailsTwo functionally active dimers are present in the asymmetric unit: Dimer 1: chains A:B Dimer 2: chains C:D

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Components

#1: Protein
17beta-hydroxysteroid dehydrogenase


Mass: 28936.545 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cochliobolus lunatus (fungus) / Strain: m118 / Gene: 17HSDcl / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O93874, 17beta-estradiol 17-dehydrogenase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GEN / GENISTEIN / 5,7-DIHYDROXY-3-(4-HYDROXYPHENYL)-4H-1-BENZOPYRAN-4-ONE / 4',5,7-TRIHYDROXYISOFLAVONE / PRUNETOL / GENISTEOL / Genistein


Mass: 270.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O5 / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% (W/v) PEG 2000 MME, 0.1M KCNS, 5 mM NADP Crystals soaked for 24 hours in: 30% (W/v) PEG 2000 MME, 0.1M KCNS, 1 mM NADP, 5% (V/V) DMSO, 2 mM genistein , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 16, 2010 / Details: Platinum coated cylindrical mirror
RadiationMonochromator: Si (1 1 1) duble crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 40171 / Num. obs: 40171 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.51
Reflection shellResolution: 2.3→2.45 Å / Redundancy: 2.52 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 4.84 / Num. unique all: 6811 / % possible all: 94.9

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Processing

Software
NameVersionClassification
XRD1beamline softwaredata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QWI

3qwi


Resolution: 2.3→46.7 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 13.834 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.526 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19881 2009 5 %RANDOM
Rwork0.15903 ---
all0.16102 38162 --
obs0.16102 38162 95.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å2-1.81 Å2
2--1.3 Å20 Å2
3----1.14 Å2
Refine analyzeLuzzati coordinate error obs: 0.242 Å
Refinement stepCycle: LAST / Resolution: 2.3→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7838 0 280 332 8450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198280
X-RAY DIFFRACTIONr_bond_other_d0.0050.025402
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.97211240
X-RAY DIFFRACTIONr_angle_other_deg1.193313144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96651035
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90823.699346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.435151290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1411548
X-RAY DIFFRACTIONr_chiral_restr0.0750.21268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029240
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021734
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A88740.08
12B88740.08
21A88780.09
22C88780.09
31A90090.07
32D90090.07
41B89510.07
42C89510.07
51B90060.06
52D90060.06
61C89420.07
62D89420.07
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 137 -
Rwork0.204 2622 -
obs-2622 91.39 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3094-0.07310.64381.1388-0.29241.96540.028-0.1701-0.21090.04350.01770.00960.2432-0.1768-0.04560.0637-0.0460.01770.06110.01360.0998-13.2273-16.526821.0579
21.24980.32650.18650.7777-0.3441.2793-0.0365-0.00430.1488-0.13140.00780.1172-0.0883-0.20410.02880.05860.0164-0.03270.0504-0.01480.0855-14.24574.101-2.5573
31.54810.5016-0.01720.9536-0.15241.6695-0.0163-0.19360.10320.1650.00230.0655-0.0735-0.0990.01390.04390.0150.01070.0555-0.02630.02076.78162.984233.6159
40.8047-0.01510.25210.9908-0.25211.4652-0.00740.07390.0327-0.1561-0.0219-0.1570.04690.10970.02930.04610.0040.02160.0209-0.00690.069815.06039.23923.9776
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 270
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A302
4X-RAY DIFFRACTION1A303
5X-RAY DIFFRACTION1D305
6X-RAY DIFFRACTION2B12 - 270
7X-RAY DIFFRACTION2B301
8X-RAY DIFFRACTION2B302
9X-RAY DIFFRACTION2B303
10X-RAY DIFFRACTION3C13 - 270
11X-RAY DIFFRACTION3C301
12X-RAY DIFFRACTION3C302 - 303
13X-RAY DIFFRACTION3C304
14X-RAY DIFFRACTION4D10 - 270
15X-RAY DIFFRACTION4D301
16X-RAY DIFFRACTION4D302
17X-RAY DIFFRACTION4D303
18X-RAY DIFFRACTION4B304
19X-RAY DIFFRACTION4D304
20X-RAY DIFFRACTION4A304

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