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- PDB-3is3: Crystal structure of 17beta-Hydroxysteroid dehydrogenase (Apo for... -

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Basic information

Entry
Database: PDB / ID: 3is3
TitleCrystal structure of 17beta-Hydroxysteroid dehydrogenase (Apo form) from fungus Cochliobolus lunatus
Components17beta-hydroxysteroid dehydrogenase
KeywordsOXIDOREDUCTASE / Hydroxysteroid dehydrogenase / Short Chain Dehydrogenase/Reductase / SDR / steroid / Fungi / Cochliobolus lunatus
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
DI(HYDROXYETHYL)ETHER / 17beta-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesCochliobolus lunatus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsCassetta, A. / Lamba, D. / Krastanova, I.
CitationJournal: To be Published
Title: Structural studies on a fungal 17beta Hydroxysteroid dehydrogenase
Authors: Cassetta, A. / Lamba, D. / Krastanova, I. / Stojan, J. / Rizner, T.L. / Kristan, K.
History
DepositionAug 25, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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)29,2065
Polymers28,9371
Non-polymers2694
Water5,332296
1
A: 17beta-hydroxysteroid dehydrogenase
hetero molecules

A: 17beta-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,41110
Polymers57,8732
Non-polymers5388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area5660 Å2
ΔGint-68 kcal/mol
Surface area20330 Å2
MethodPISA
2
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)116,82320
Polymers115,7464
Non-polymers1,07616
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 area17420 Å2
ΔGint-166 kcal/mol
Surface area34550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.914, 67.914, 268.347
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#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
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 53.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% (W/V) PEG 6000, 20% (V/V) Glycerol, 0.1M Tris, 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: 1.2 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 20, 2005 / Details: Platinum Coated three segment toroidal mirror
RadiationMonochromator: Double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.48→28.8 Å / Num. all: 52140 / Num. obs: 52140 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 19.2
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1894 / Rsym value: 0.494 / % possible all: 98.4

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0094refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G0O

1g0o


Resolution: 1.48→23.86 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.389 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.067 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18828 5215 10.1 %RANDOM
Rwork0.17495 ---
all0.17633 51846 --
obs0.17633 51846 98.36 %-
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: 24.853 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.48→23.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 15 296 2275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212055
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.942778
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0415264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39423.63688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.11315326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4261512
X-RAY DIFFRACTIONr_chiral_restr0.1040.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211554
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_it0.7731.51303
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.30422087
X-RAY DIFFRACTIONr_scbond_it2.2273752
X-RAY DIFFRACTIONr_scangle_it3.5294.5690
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.482→1.521 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 328 -
Rwork0.303 3041 -
obs-3041 87.99 %
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)
11.3373-0.519-0.0410.89290.05251.1982-0.0358-0.07030.13210.0607-0.02050.0064-0.219-0.12750.05630.0830.0095-0.0090.0539-0.02110.0911-9.97112.54717.693
21.820.8559-0.00652.0189-0.08681.5441-0.0335-0.04720.07460.0101-0.0507-0.2765-0.32020.12490.08420.1242-0.0151-0.03570.0365-0.00720.1174-0.50418.4244.796
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 208
2X-RAY DIFFRACTION2A209 - 270

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