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- PDB-4fiz: Crystal structure of the binary complex between a fungal 17beta-h... -

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Basic information

Entry
Database: PDB / ID: 4fiz
TitleCrystal structure of the binary complex between a fungal 17beta-hydroxysteroid dehydrogenase (Apo form) and coumestrol
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
Coumestrol / 17beta-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesCochliobolus lunatus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCassetta, A. / Lamba, D. / Krastanova, I.
CitationJournal: To be Published
Title: Crystallographic studies on the flavonoid inhibition of a fungal 17beta-hydroxysteroid dehydrogenase
Authors: Cassetta, A. / Lamba, D. / Krastanova, I. / Kristan, K. / Brunskole-Svegelj, M. / Stojan, J. / Lanisnik-Rizner, T.
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 1.2Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7799
Polymers28,9371
Non-polymers8428
Water2,936163
1
A: 17beta-hydroxysteroid dehydrogenase
hetero molecules

A: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,55818
Polymers57,8732
Non-polymers1,68516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area5860 Å2
ΔGint-45 kcal/mol
Surface area20440 Å2
MethodPISA
2
A: 17beta-hydroxysteroid dehydrogenase
hetero molecules

A: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,55818
Polymers57,8732
Non-polymers1,68516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area5180 Å2
ΔGint-41 kcal/mol
Surface area21130 Å2
MethodPISA
3
A: 17beta-hydroxysteroid dehydrogenase
hetero molecules

A: 17beta-hydroxysteroid dehydrogenase
hetero molecules

A: 17beta-hydroxysteroid dehydrogenase
hetero molecules

A: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,11536
Polymers115,7464
Non-polymers3,36932
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area19250 Å2
ΔGint-122 kcal/mol
Surface area34230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.920, 67.920, 267.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-423-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 17beta-hydroxysteroid dehydrogenase


Mass: 28936.545 Da / Num. of mol.: 1
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): JM107
References: UniProt: O93874, 17beta-estradiol 17-dehydrogenase

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Non-polymers , 5 types, 171 molecules

#2: Chemical ChemComp-CUE / Coumestrol / 3,9-dihydroxy-6H-[1]benzofuro[3,2-c]chromen-6-one / Coumestrol


Mass: 268.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H8O5
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% (W/V) PEG 6000, 20% (V/V) Glycerol, 0.1 M Tris Soaked for 24 hours with: 20% (W/V) PEG 6000, 20% (V/V) Glycerol, 0.1 M Tris 2 mM coumestrol. 5% DMSO in the soaking solution, pH 8.0, ...Details: 20% (W/V) PEG 6000, 20% (V/V) Glycerol, 0.1 M Tris Soaked for 24 hours with: 20% (W/V) PEG 6000, 20% (V/V) Glycerol, 0.1 M Tris 2 mM coumestrol. 5% DMSO in the soaking solution, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2010 / Details: Platinum coated cylindrical mirror
RadiationMonochromator: Double crystal Si(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 24719 / Num. obs: 24719 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 11.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 2.5 % / Rmerge(I) obs: 3.2 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1249 / Rsym value: 0.203 / % possible all: 82.7

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Processing

Software
NameVersionClassification
XRD1beamline softwaredata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IS3

3is3


Resolution: 1.9→19.7 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.289 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17185 1236 5 %RANDOM
Rwork0.1556 ---
all0.15641 23482 --
obs0.15641 23482 97.39 %-
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: 32.813 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2--1.35 Å20 Å2
3----2.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 55 163 2182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192087
X-RAY DIFFRACTIONr_bond_other_d0.0010.021991
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.9592821
X-RAY DIFFRACTIONr_angle_other_deg0.77134558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1065263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46623.63688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98215326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9881512
X-RAY DIFFRACTIONr_chiral_restr0.0790.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022374
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02481
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 76 -
Rwork0.223 1458 -
obs-1534 83.55 %
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)
11.0562-0.5075-0.76762.7352-0.31825.7266-0.0614-0.0799-0.263-0.1754-0.0935-0.05590.63780.22390.15490.25530.06350.02160.13980.05470.086716.672-22.187716.4765
21.743-0.3797-0.1250.8671-0.11721.4395-0.0651-0.1003-0.08480.1043-0.0202-0.0060.16780.15240.08520.1214-0.02560.00690.07730.02270.01078.3073-8.620718.2998
347.0297-16.37970.731613.74151.33642.0282-0.7203-1.02790.36571.12410.0391-0.2716-0.09950.38030.68130.5385-0.12510.00660.36270.12810.3538-5.6474-23.357314.9341
40.71440.21260.01582.06610.29722.5876-0.0202-0.0922-0.12370.1389-0.12250.33410.4716-0.22740.14270.2059-0.04590.0560.08350.00140.09660.5803-18.26555.1711
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 63
2X-RAY DIFFRACTION1A308
3X-RAY DIFFRACTION2A64 - 201
4X-RAY DIFFRACTION2A302 - 305
5X-RAY DIFFRACTION2A307
6X-RAY DIFFRACTION3A202 - 207
7X-RAY DIFFRACTION3A306
8X-RAY DIFFRACTION4A208 - 270
9X-RAY DIFFRACTION4A301

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