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- PDB-6ucy: Multi-conformer model of Ketosteroid Isomerase from Pseudomonas P... -

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Basic information

Entry
Database: PDB / ID: 6ucy
TitleMulti-conformer model of Ketosteroid Isomerase from Pseudomonas Putida (pKSI) bound to 4-Androstenedione at 250 K
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE
Function / homologyKetosteroid isomerase / steroid Delta-isomerase / SnoaL-like domain / SnoaL-like domain / steroid delta-isomerase activity / steroid metabolic process / NTF2-like domain superfamily / 4-ANDROSTENE-3-17-DIONE / Steroid Delta-isomerase
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsYabukarski, F. / Herschlag, D. / Biel, J.T. / Fraser, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1714723 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles.
Authors: Yabukarski, F. / Biel, J.T. / Pinney, M.M. / Doukov, T. / Powers, A.S. / Fraser, J.S. / Herschlag, D.
History
DepositionSep 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,7898
Polymers29,0972
Non-polymers6926
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-49 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.061, 73.852, 95.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14548.501 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Production host: Escherichia coli (E. coli) / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical ChemComp-ASD / 4-ANDROSTENE-3-17-DIONE / Androstenedione


Mass: 286.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H26O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 17-23% PEG 3350, 0.2 M MAGNESIUM CHLORIDE / Temp details: room temperature

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Data collection

DiffractionMean temperature: 250 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.15→36.06 Å / Num. obs: 89597 / % possible obs: 98.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 11.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.029 / Rrim(I) all: 0.075 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.15-1.176.51.50442120.5830.6261.63294.4
6.3-36.066.30.0366550.9980.0160.0499.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VSY

3vsy


Resolution: 1.15→32.404 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1636 4435 4.99 %
Rwork0.1459 84531 -
obs0.1468 88966 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.2 Å2 / Biso mean: 17.1509 Å2 / Biso min: 4.68 Å2
Refinement stepCycle: final / Resolution: 1.15→32.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 145 314 2466
Biso mean--22.18 28.61 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095102
X-RAY DIFFRACTIONf_angle_d1.0956856
X-RAY DIFFRACTIONf_chiral_restr0.079736
X-RAY DIFFRACTIONf_plane_restr0.007901
X-RAY DIFFRACTIONf_dihedral_angle_d14.4851912
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.1503-1.16330.25951450.2672268994
1.1633-1.1770.29331490.265268495
1.177-1.19140.27531370.2567277196
1.1914-1.20650.28161710.2578272596
1.2065-1.22230.30411310.2623274396
1.2223-1.23910.24811570.2568275997
1.2391-1.25680.26211440.2274276897
1.2568-1.27550.22461530.2175276897
1.2755-1.29550.22711510.2056277297
1.2955-1.31670.23121460.1976280198
1.3167-1.33940.2111490.1895283897
1.3394-1.36380.18471410.1765277497
1.3638-1.390.18371480.1694280298
1.39-1.41840.22181520.1699273996
1.4184-1.44920.20771520.1588282697
1.4492-1.48290.17631410.1514279798
1.4829-1.520.14661560.1392285698
1.52-1.56110.14331360.1238283298
1.5611-1.6070.12791410.1175284498
1.607-1.65890.13851470.1164285599
1.6589-1.71820.1541570.117286999
1.7182-1.7870.13231430.1149278997
1.787-1.86830.15191420.1162287799
1.8683-1.96680.13511600.1147287899
1.9668-2.090.13061560.1174289499
2.09-2.25130.12711310.1119294699
2.2513-2.47780.15621360.1234289699
2.4778-2.83620.15771520.1346288497
2.8362-3.57260.14191590.1397292498
3.5726-32.4040.16011520.1546293193

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