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- PDB-4fj2: Crystal structure of the ternary complex between a fungal 17beta-... -

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Basic information

Entry
Database: PDB / ID: 4fj2
TitleCrystal structure of the ternary complex between a fungal 17beta-hydroxysteroid dehydrogenase (Holo form) and biochanin A
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


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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-QSO / 17beta-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesCochliobolus lunatus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)119,59915
Polymers115,7464
Non-polymers3,85211
Water3,549197
1
A: 17beta-hydroxysteroid dehydrogenase
B: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7687
Polymers57,8732
Non-polymers1,8955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-17 kcal/mol
Surface area19260 Å2
MethodPISA
2
C: 17beta-hydroxysteroid dehydrogenase
D: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8308
Polymers57,8732
Non-polymers1,9576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-16 kcal/mol
Surface area19320 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21780 Å2
ΔGint-70 kcal/mol
Surface area31830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.430, 115.280, 69.600
Angle α, β, γ (deg.)90.00, 102.93, 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: _ / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA11 - 27011 - 270
21TYRTYRBB11 - 27011 - 270
12PROPROAA13 - 26913 - 269
22PROPROCC13 - 26913 - 269
13TYRTYRAA11 - 26911 - 269
23TYRTYRDD11 - 26911 - 269
14PROPROBB13 - 26913 - 269
24PROPROCC13 - 26913 - 269
15TYRTYRBB11 - 26911 - 269
25TYRTYRDD11 - 26911 - 269
16PROPROCC13 - 26913 - 269
26PROPRODD13 - 26913 - 269

NCS ensembles :
ID
1
2
3
4
5
6

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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


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-QSO / 5,7-dihydroxy-3-(4-methoxyphenyl)-4H-chromen-4-one / Biochanin A


Mass: 284.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% (W/V) PEG 2000 MME, 0.1M KCNS, 5mM NADP, Crystals soaked for 24 hours in: 30% (W/V) PEG 2000 MME, 0.1M KCNS, 1mM NADP, 5% (V/V) DMSO, 2 mM biochanin A , pH 7.0, VAPOR DIFFUSION, HANGING ...Details: 30% (W/V) PEG 2000 MME, 0.1M KCNS, 5mM NADP, Crystals soaked for 24 hours in: 30% (W/V) PEG 2000 MME, 0.1M KCNS, 1mM NADP, 5% (V/V) DMSO, 2 mM biochanin A , 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) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. all: 32695 / Num. obs: 32695 / % possible obs: 76.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 19
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2.27 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 6.63 / Num. unique all: 1574 / % possible all: 50.1

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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: pdb entry 3QWI

3qwi


Resolution: 2.5→33.43 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 19.135 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20801 1352 5 %RANDOM
Rwork0.16641 ---
all0.16853 25680 --
obs0.16853 25680 81.28 %-
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: 27.813 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å2-1.28 Å2
2--2.54 Å20 Å2
3----1.47 Å2
Refine analyzeLuzzati coordinate error obs: 0.278 Å
Refinement stepCycle: LAST / Resolution: 2.5→33.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7843 0 254 197 8294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198307
X-RAY DIFFRACTIONr_bond_other_d0.0050.025449
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.97311281
X-RAY DIFFRACTIONr_angle_other_deg1.237313249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66151038
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71123.707348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.533151294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6021548
X-RAY DIFFRACTIONr_chiral_restr0.0730.21257
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029295
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021748
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A90060.07
12B90060.07
21A89200.07
22C89200.07
31A88970.07
32D88970.07
41B89850.08
42C89850.08
51B90150.09
52D90150.09
61C88430.08
62D88430.08
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 92 -
Rwork0.236 1733 -
obs-1733 76.23 %
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)
11.5865-0.03440.7511.2258-0.12051.750.0237-0.1497-0.27020.03270.0145-0.0050.2625-0.1676-0.03820.1113-0.06550.00970.09210.0080.1401-13.2199-27.860420.7303
21.63090.45670.20711.0703-0.51841.12-0.03020.0750.1342-0.07890.02990.1041-0.1248-0.21030.00030.07370.0128-0.00760.099-0.00630.0923-14.2943-6.9792-2.9333
31.24530.7386-0.29960.9519-0.18851.9267-0.0107-0.17950.1080.16120.01850.0745-0.1033-0.132-0.00780.09940.0234-0.00450.0941-0.01880.07236.5285-8.050933.4427
40.91250.25070.16421.2401-0.0271.4093-0.02770.1223-0.0059-0.10930.0314-0.16030.02980.1138-0.00370.0633-0.00210.0120.0387-0.00480.095814.8862-1.57063.8932
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 270
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A302
4X-RAY DIFFRACTION2B11 - 270
5X-RAY DIFFRACTION2B301
6X-RAY DIFFRACTION2B302
7X-RAY DIFFRACTION2B303
8X-RAY DIFFRACTION3C13 - 270
9X-RAY DIFFRACTION3C301
10X-RAY DIFFRACTION3C302
11X-RAY DIFFRACTION4D10 - 270
12X-RAY DIFFRACTION4D301
13X-RAY DIFFRACTION4D302
14X-RAY DIFFRACTION4C303
15X-RAY DIFFRACTION4D303

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