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- PDB-3t8u: Crystal structure of ketosteroid isomerase Y14AY55FD99A from Pseu... -

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Basic information

Entry
Database: PDB / ID: 3t8u
TitleCrystal structure of ketosteroid isomerase Y14AY55FD99A from Pseudomonas testosteroni
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE
Function / homology
Function and homology information


steroid Delta-isomerase / steroid delta-isomerase activity / steroid metabolic process
Similarity search - Function
Steroid delta5-4-isomerase / Ketosteroid isomerase / Nuclear transport factor 2 (NTF2) domain / SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Steroid Delta-isomerase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsGonzalez, A. / Tsai, Y. / Schwans, J. / Sunden, F. / Herschlag, D.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Evaluating the catalytic contribution from the oxyanion hole in ketosteroid isomerase.
Authors: Schwans, J.P. / Sunden, F. / Gonzalez, A. / Tsai, Y. / Herschlag, D.
History
DepositionAug 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,90513
Polymers53,0404
Non-polymers8659
Water1,06359
1
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8085
Polymers26,5202
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-41 kcal/mol
Surface area12390 Å2
MethodPISA
2
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0968
Polymers26,5202
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-73 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.227, 64.227, 496.554
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
Steroid Delta-isomerase / Delta(5)-3-ketosteroid isomerase


Mass: 13259.996 Da / Num. of mol.: 4 / Mutation: Y14A, Y55F, D99A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Gene: ksi / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00947, steroid Delta-isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 2.0 M ammonium sulfate, 40 mM potassium phosphate, 1 mM EDTA, 2 mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2011
RadiationMonochromator: Si single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→38.196 Å / Num. all: 22525 / Num. obs: 22525 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rsym value: 0.077 / Net I/σ(I): 21.9
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.646.80.72079930611.11697
2.64-2.810.21.13110730400.74199.9
2.8-2.99111.73123228290.457100
2.99-3.2311.53.33097426880.238100
3.23-3.5411.76.22931524950.125100
3.54-3.9611.610.32621322560.074100
3.96-4.5711.415.42345420520.046100
4.57-5.610.916.61925817620.04100
5.6-7.9110.417.71490814370.036100
7.91-38.1969.123.981929050.02498.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M8C

3m8c


Resolution: 2.5→35.05 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.884 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 30.672 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3001 1145 5.1 %RANDOM
Rwork0.2386 ---
all0.2416 22369 --
obs0.2416 22369 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 216.37 Å2 / Biso mean: 62.921 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-3.43 Å21.72 Å20 Å2
2--3.43 Å20 Å2
3----5.15 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 45 59 3812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223905
X-RAY DIFFRACTIONr_bond_other_d0.0010.022562
X-RAY DIFFRACTIONr_angle_refined_deg1.331.955309
X-RAY DIFFRACTIONr_angle_other_deg0.81836226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2965508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34923.523176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.1915604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6361531
X-RAY DIFFRACTIONr_chiral_restr0.0790.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02832
X-RAY DIFFRACTIONr_mcbond_it0.4191.52509
X-RAY DIFFRACTIONr_mcbond_other0.0891.51018
X-RAY DIFFRACTIONr_mcangle_it0.77724011
X-RAY DIFFRACTIONr_scbond_it1.33231396
X-RAY DIFFRACTIONr_scangle_it2.1864.51298
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 78 -
Rwork0.345 1429 -
all-1507 -
obs--93.02 %
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)
12.9067-0.41561.13850.96490.58032.7396-0.015-0.11040.34060.2344-0.0683-0.13620.0145-0.20370.08330.74480.1233-0.12230.072-0.05540.268-19.5001-13.1164-48.3128
22.624-1.10541.53561.1306-1.45222.20460.0865-0.13640.35380.0213-0.2397-0.084-0.51030.3690.15320.8055-0.1156-0.14740.1843-0.1130.31212.3055-21.5531-44.2711
32.16530.1541-0.25071.66560.74634.9701-0.1388-0.3399-0.16540.29470.01790.19120.6364-0.26290.12090.11610.01560.03650.4725-0.12030.285-3.6448-37.60523.9746
42.99460.03350.32761.78690.73874.987-0.13330.0419-0.0262-0.20.19890.06970.15660.332-0.06560.0421-0.0147-0.01690.3761-0.14440.20211.2703-35.22-14.3738
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 123
2X-RAY DIFFRACTION1A126 - 128
3X-RAY DIFFRACTION1A129 - 140
4X-RAY DIFFRACTION2B1 - 124
5X-RAY DIFFRACTION2B126 - 136
6X-RAY DIFFRACTION3C1 - 124
7X-RAY DIFFRACTION3C126 - 128
8X-RAY DIFFRACTION3C129 - 148
9X-RAY DIFFRACTION4D1 - 124
10X-RAY DIFFRACTION4D126 - 128
11X-RAY DIFFRACTION4D129 - 144

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