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- PDB-3ipt: Crystal Structure of Ketosteroid Isomerase Y16S/D40N from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 3ipt
TitleCrystal Structure of Ketosteroid Isomerase Y16S/D40N from Pseudomonas putida with Bound Equilenin
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE / enzyme-ligand complex / protein cavity / Lipid metabolism / Steroid metabolism
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
EQUILENIN / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.632 Å
AuthorsFenn, T.D. / Sigala, P.A. / Herschlag, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole.
Authors: Kraut, D.A. / Sigala, P.A. / Fenn, T.D. / Herschlag, D.
History
DepositionAug 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 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 1.3Sep 6, 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

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)58,9518
Polymers57,8864
Non-polymers1,0654
Water3,981221
1
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4764
Polymers28,9432
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-11 kcal/mol
Surface area12620 Å2
MethodPISA
2
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4764
Polymers28,9432
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-11 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.694, 72.401, 81.328
Angle α, β, γ (deg.)90.000, 91.160, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 2:61 or resseq 65:127 )
211chain B and (resseq 2:61 or resseq 65:127 )
311chain C and (resseq 2:61 or resseq 65:127 )
411chain D and (resseq 2:61 or resseq 65:127 )
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D).

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Components

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


Mass: 14471.419 Da / Num. of mol.: 4 / Mutation: Y16S,D40N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Plasmid: pET21c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical
ChemComp-EQU / EQUILENIN / Equilenin


Mass: 266.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H18O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.9 M ammonium sulfate, 40 mM potassium phosphate, pH 7.2, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2008
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→43.41 Å / Num. obs: 60155 / % possible obs: 82.3 % / Biso Wilson estimate: 22.09 Å2 / Rmerge(I) obs: 0.166 / Net I/σ(I): 9.7
Reflection shellHighest resolution: 1.63 Å / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 9.7

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2PZV

2pzv


Resolution: 1.632→43.408 Å / Occupancy max: 1 / Occupancy min: 0.31 / SU ML: 1.29 / Isotropic thermal model: Isotropic / σ(F): 0.09 / Phase error: 30.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 3023 5.03 %
Rwork0.207 --
obs0.2089 60155 82.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.762 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 50.786 Å2
Baniso -1Baniso -2Baniso -3
1--13.861 Å2-0 Å23.965 Å2
2---10.001 Å2-0 Å2
3---7.375 Å2
Refinement stepCycle: LAST / Resolution: 1.632→43.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3827 0 80 221 4128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0314175
X-RAY DIFFRACTIONf_angle_d2.6965702
X-RAY DIFFRACTIONf_dihedral_angle_d18.5721548
X-RAY DIFFRACTIONf_chiral_restr0.211604
X-RAY DIFFRACTIONf_plane_restr0.015761
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A894X-RAY DIFFRACTIONPOSITIONAL
12B894X-RAY DIFFRACTIONPOSITIONAL0.225
13C971X-RAY DIFFRACTIONPOSITIONAL0.182
14D923X-RAY DIFFRACTIONPOSITIONAL0.191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6322-1.65770.3473390.2875784X-RAY DIFFRACTION25
1.6577-1.68480.3267520.27571162X-RAY DIFFRACTION37
1.6848-1.71390.304770.28511323X-RAY DIFFRACTION43
1.7139-1.74510.29851030.26661658X-RAY DIFFRACTION53
1.7451-1.77860.32381090.25881896X-RAY DIFFRACTION61
1.7786-1.81490.33461280.26162182X-RAY DIFFRACTION70
1.8149-1.85440.28751230.26882444X-RAY DIFFRACTION78
1.8544-1.89750.32361380.25742636X-RAY DIFFRACTION84
1.8975-1.9450.32071410.24382911X-RAY DIFFRACTION92
1.945-1.99760.28331680.24542914X-RAY DIFFRACTION94
1.9976-2.05630.29121450.23263016X-RAY DIFFRACTION95
2.0563-2.12270.25621410.23373024X-RAY DIFFRACTION96
2.1227-2.19860.27121710.20983042X-RAY DIFFRACTION96
2.1986-2.28660.26221560.2063035X-RAY DIFFRACTION97
2.2866-2.39070.23541680.20513092X-RAY DIFFRACTION98
2.3907-2.51670.26181630.21463096X-RAY DIFFRACTION98
2.5167-2.67440.22821600.21483111X-RAY DIFFRACTION98
2.6744-2.88080.29141590.23373119X-RAY DIFFRACTION99
2.8808-3.17060.25711750.21493175X-RAY DIFFRACTION100
3.1706-3.62920.21241660.1873153X-RAY DIFFRACTION99
3.6292-4.57170.18791710.1663143X-RAY DIFFRACTION99
4.5717-43.42360.22241700.18213217X-RAY DIFFRACTION99
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.47910.07790.11050.7277-0.41570.42730.0105-0.0310.10630.0313-0.1082-0.19670.04020.17430.06530.14960.0042-0.0070.1935-0.01780.206112.9794-5.67050.869
21.12850.02370.19380.8596-0.18781.2088-0.0586-0.15540.03950.03310.06230.29760.0036-0.1997-0.01720.12720.00160.00580.17430.00730.2205
36.46520.5025-1.76250.34250.46022.5891-0.25050.26840.2940.0221-0.06410.29990.1882-0.28230.24980.2443-0.01690.02390.25980.02030.3553
47.2589-0.7182-1.29480.1957-0.22981.3795-0.1420.64510.3691-0.0350.0357-0.25290.01660.22370.06070.2378-0.03330.02880.40530.00660.4322
Refinement TLS groupSelection details: chain D

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