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- PDB-3t8n: Crystal structure of ketosteroid isomerase Y16AD103A from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 3t8n
TitleCrystal structure of ketosteroid isomerase Y16AD103A from Pseudomonas putida
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE
Function / homology
Function and homology information


steroid Delta-isomerase / steroid Delta-isomerase activity / steroid metabolic process
Similarity search - Function
Ketosteroid isomerase / 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
Chem-EDT / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: Steroid Delta-isomerase
F: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,42210
Polymers57,6504
Non-polymers7736
Water3,855214
1
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0174
Polymers28,8252
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-31 kcal/mol
Surface area12710 Å2
MethodPISA
2
D: Steroid Delta-isomerase
F: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4056
Polymers28,8252
Non-polymers5804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-53 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.514, 76.644, 53.060
Angle α, β, γ (deg.)90.000, 63.960, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 14412.394 Da / Num. of mol.: 4 / Mutation: Y16A, D103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 1.6 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: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2011
RadiationMonochromator: Si single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.465→38.322 Å / Num. all: 77168 / Num. obs: 77168 / % possible obs: 98 % / Redundancy: 3.6 % / Rsym value: 0.038 / Net I/σ(I): 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.46-1.543.20.8720.932348101030.87288.4
1.54-1.643.70.4931.639805108430.49399.8
1.64-1.753.70.2982.637476101610.29899.8
1.75-1.893.70.15953511094910.15999.9
1.89-2.073.70.0839.53235387230.08399.8
2.07-2.323.70.04815.82941379300.04899.9
2.32-2.673.70.03421.32584469630.03499.9
2.67-3.283.70.02427.32163459120.02499.8
3.28-4.633.60.017371642645740.01799.5
4.63-38.3223.60.01443.8891924680.01496.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.82 Å38.32 Å
Translation1.82 Å38.32 Å

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Processing

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

3rgr


Resolution: 1.47→38.32 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.2106 / WRfactor Rwork: 0.1767 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8433 / SU B: 3.692 / SU ML: 0.061 / SU R Cruickshank DPI: 0.0813 / SU Rfree: 0.0824 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 3852 5 %RANDOM
Rwork0.1859 ---
all0.1876 77108 --
obs0.1876 77108 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 98.98 Å2 / Biso mean: 27.0688 Å2 / Biso min: 7.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.18 Å2
2--0.8 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.47→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3955 0 45 214 4214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214550
X-RAY DIFFRACTIONr_bond_other_d0.0020.023073
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.956234
X-RAY DIFFRACTIONr_angle_other_deg0.9343.0017452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3323.915235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35415737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6451547
X-RAY DIFFRACTIONr_chiral_restr0.0950.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215427
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02952
X-RAY DIFFRACTIONr_mcbond_it0.9341.52838
X-RAY DIFFRACTIONr_mcbond_other0.2561.51146
X-RAY DIFFRACTIONr_mcangle_it1.65224611
X-RAY DIFFRACTIONr_scbond_it2.35431712
X-RAY DIFFRACTIONr_scangle_it3.7194.51621
LS refinement shellResolution: 1.47→1.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 253 -
Rwork0.391 4448 -
all-4701 -
obs--81.11 %
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)
11.7720.05530.2440.3341-0.08471.23110.0113-0.21940.02840.077-0.0406-0.0335-0.028-0.02320.02930.02650.00490.010.1349-0.01340.0623-11.582-36.55913.932
21.15690.1973-0.07660.35790.0630.8772-0.04170.174-0.0134-0.0670.01140.01650.0032-0.13760.03020.0199-0.00320.01670.1461-0.01190.0551-20.273-39.897-7.513
31.46890.195-0.43220.96140.0391.5810.0516-0.2087-0.06310.133-0.0406-0.07030.07010.0209-0.0110.03270.01520.00540.1830.02130.0482-60.874-34.147-24.256
41.45480.7016-0.99562.8416-1.21442.3362-0.0760.4080.0894-0.36610.28180.26050.1927-0.5864-0.20580.0506-0.0274-0.03090.33170.05270.0587-67.783-32.484-46.225
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 130
2X-RAY DIFFRACTION2B2 - 131
3X-RAY DIFFRACTION3D1 - 127
4X-RAY DIFFRACTION4F1 - 130

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