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- PDB-3itd: Crystal structure of an inactive 17beta-Hydroxysteroid dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 3itd
TitleCrystal structure of an inactive 17beta-Hydroxysteroid dehydrogenase (Y167F mutated 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


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
17beta-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesCochliobolus lunatus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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. / Lanisnik Rizner, T. / Kristan, K.
History
DepositionAug 28, 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 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 17beta-Hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0483
Polymers28,9211
Non-polymers1282
Water3,495194
1
A: 17beta-Hydroxysteroid dehydrogenase
hetero molecules

A: 17beta-Hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0966
Polymers57,8412
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area4470 Å2
ΔGint-46 kcal/mol
Surface area21050 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)116,19212
Polymers115,6824
Non-polymers5108
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 area15180 Å2
ΔGint-128 kcal/mol
Surface area35850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.790, 67.790, 269.930
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: 28920.545 Da / Num. of mol.: 1 / Mutation: Y167F
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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
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, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 19, 2006 / Details: Pt coated Si Mirror (KB geometry)
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.89→39.1 Å / Num. all: 25756 / Num. obs: 25756 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 15.8
Reflection shellResolution: 1.89→2 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 5.2 / Num. unique all: 3690 / Rsym value: 0.345 / % possible all: 100

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Processing

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

3is3


Resolution: 1.89→33.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.26 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.12 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18906 1308 5.1 %RANDOM
Rwork0.1675 ---
all0.1686 25722 --
obs0.1686 25722 99.98 %-
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: 25.192 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.242 Å
Refinement stepCycle: LAST / Resolution: 1.89→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 7 194 2164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212010
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9342720
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21823.67887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87415323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9641512
X-RAY DIFFRACTIONr_chiral_restr0.1040.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211525
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_it0.6911.51283
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22822054
X-RAY DIFFRACTIONr_scbond_it2.0883727
X-RAY DIFFRACTIONr_scangle_it3.3494.5665
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 99 -
Rwork0.214 1758 -
obs-1857 100 %
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)
11.5544-0.5838-0.02290.99660.06681.4191-0.0653-0.07790.1920.0971-0.0340.0062-0.2853-0.16560.09940.0980.0103-0.0150.0534-0.03560.0484-9.80612.7117.908
22.01591.05120.41022.8319-0.53122.5039-0.1059-0.07090.08630.0003-0.1358-0.4131-0.4740.1610.24170.128-0.0155-0.04660.02290.01360.1081-0.5318.4984.72
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 208
2X-RAY DIFFRACTION2A209 - 270

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