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- PDB-3qwf: Crystal structure of the 17beta-hydroxysteroid dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 3qwf
TitleCrystal structure of the 17beta-hydroxysteroid dehydrogenase from Cochliobolus lunatus
Components17beta-hydroxysteroid dehydrogenase
KeywordsOXIDOREDUCTASE / HYDROXYSTEROID DEHYDROGENASE / SHORT CHAIN DEHYDROGENASE/REDUCTASE / SDR STEROID / FUNGI / COCHLIOBOLUS LUNATUS / Rossmann Fold / Cytosol
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 / 17beta-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesCochliobolus lunatus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsCassetta, A. / Lamba, D. / Krastanova, I. / Stojan, J. / Lanisnik-Rizner, T. / Kristan, K. / Brunskole, M.
CitationJournal: Biochem.J. / Year: 2012
Title: Structural Studies on a Fungal 17Beta-Hydroxysteroid Dehydrogenase
Authors: Cassetta, A. / Krastanova, I. / Kristan, K. / Brunskole Svegelj, M. / Lamba, D. / Lanisnik Rizner, T. / Stojan, J.
History
DepositionFeb 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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
B: 17beta-hydroxysteroid dehydrogenase
C: 17beta-hydroxysteroid dehydrogenase
D: 17beta-hydroxysteroid dehydrogenase
E: 17beta-hydroxysteroid dehydrogenase
F: 17beta-hydroxysteroid dehydrogenase
G: 17beta-hydroxysteroid dehydrogenase
H: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,36126
Polymers231,4928
Non-polymers6,86818
Water23,6721314
1
A: 17beta-hydroxysteroid dehydrogenase
B: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7288
Polymers57,8732
Non-polymers1,8556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-32 kcal/mol
Surface area19950 Å2
MethodPISA
2
C: 17beta-hydroxysteroid dehydrogenase
D: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5446
Polymers57,8732
Non-polymers1,6714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-32 kcal/mol
Surface area20210 Å2
MethodPISA
3
E: 17beta-hydroxysteroid dehydrogenase
F: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5446
Polymers57,8732
Non-polymers1,6714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-31 kcal/mol
Surface area19840 Å2
MethodPISA
4
G: 17beta-hydroxysteroid dehydrogenase
H: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5446
Polymers57,8732
Non-polymers1,6714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-30 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.520, 67.830, 138.890
Angle α, β, γ (deg.)84.20, 85.31, 66.57
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
17beta-hydroxysteroid dehydrogenase


Mass: 28936.545 Da / Num. of mol.: 8
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
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1314 / 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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: 20% (W/V) PEG 6000, 25% (V/V) GLYCEROL, 0.1M TRIS, 5MM NADPH SODIUM SALT, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2008 / Details: RH COATED, SILICON TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI (111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.88→53.4 Å / Num. all: 170185 / Num. obs: 170185 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 10.1
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.526 / % possible all: 94.9

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0094refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3IS3

3is3


Resolution: 1.88→37.45 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 7.318 / SU ML: 0.096 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19438 8540 5 %RANDOM
Rwork0.16514 ---
obs0.16663 161632 95.95 %-
all-170171 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0.07 Å20.01 Å2
2--0.02 Å2-0.01 Å2
3----0.11 Å2
Refine analyzeLuzzati coordinate error obs: 0.284 Å
Refinement stepCycle: LAST / Resolution: 1.88→37.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15768 0 444 1314 17526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02216546
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.96822466
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60852080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03423.678696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.386152592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9671596
X-RAY DIFFRACTIONr_chiral_restr0.0790.22528
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02112392
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3891.510280
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.701216472
X-RAY DIFFRACTIONr_scbond_it1.1736266
X-RAY DIFFRACTIONr_scangle_it1.8414.55994
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 570 -
Rwork0.314 11774 -
obs--93.76 %
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)
12.1539-0.48820.44451.4064-0.10511.83260.0444-0.28170.03370.09210.0298-0.20840.12650.2783-0.07420.0915-0.0143-0.04050.1416-0.02070.14521.12780.4662-1.521
21.9956-0.09480.71411.2117-0.06922.075-0.1059-0.34350.29660.0882-0.00750.0452-0.2334-0.29420.11330.10310.0123-0.00780.0905-0.08760.1939-20.415820.6787-9.4822
31.6416-0.17230.78151.60530.2852.24790.03930.52820.1147-0.3242-0.0555-0.1659-0.06150.31090.01620.1728-0.01170.03620.18340.03290.1205-15.357610.5779-39.1094
41.9553-0.01551.291.3276-0.10562.17780.42950.3098-0.5947-0.1397-0.0350.05910.74980.2065-0.39450.3730.0839-0.14480.0676-0.1260.3176-9.7944-16.482-26.3076
51.4463-0.3831-0.41661.43590.27511.83610.1020.24020.2512-0.1524-0.074-0.0808-0.3199-0.0254-0.0280.2014-0.00540.00660.20530.09320.1618-34.728323.063742.7451
61.5105-0.4607-0.18751.3067-0.04561.8435-0.13-0.2694-0.09870.17380.07460.16930.0145-0.19550.05540.14470.00160.05110.24260.03560.1193-40.16910.063871.3266
71.6737-0.7953-0.48121.34840.29132.1323-0.03440.3943-0.2711-0.122-0.14430.26950.1976-0.26020.17860.164-0.064-0.00230.2663-0.04350.1657-29.9849-5.833433.3943
81.5657-0.6361-0.48460.93510.6991.9974-0.2348-0.2819-0.19530.19870.1124-0.0360.34390.36190.12240.22660.05650.05520.23030.10710.1703-18.9526-10.324862.8917
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C10 - 270
2X-RAY DIFFRACTION1C273
3X-RAY DIFFRACTION1C274 - 1307
4X-RAY DIFFRACTION2A10 - 270
5X-RAY DIFFRACTION2A273
6X-RAY DIFFRACTION2A274 - 1307
7X-RAY DIFFRACTION3B10 - 270
8X-RAY DIFFRACTION3B272
9X-RAY DIFFRACTION3B274 - 1311
10X-RAY DIFFRACTION4D10 - 270
11X-RAY DIFFRACTION4D272
12X-RAY DIFFRACTION4D274 - 1308
13X-RAY DIFFRACTION5E10 - 270
14X-RAY DIFFRACTION5E272
15X-RAY DIFFRACTION5E273 - 1300
16X-RAY DIFFRACTION6F10 - 270
17X-RAY DIFFRACTION6F272
18X-RAY DIFFRACTION6F273 - 1309
19X-RAY DIFFRACTION7G10 - 270
20X-RAY DIFFRACTION7G272
21X-RAY DIFFRACTION8H10 - 270
22X-RAY DIFFRACTION8H272
23X-RAY DIFFRACTION8H273 - 1286

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