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

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Basic information

Entry
Database: PDB / ID: 6ucn
TitleMulti-conformer model of Ketosteroid Isomerase from Pseudomonas Putida (pKSI) bound to Equilenin at 250 K
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE
Function / homologyKetosteroid isomerase / steroid Delta-isomerase / SnoaL-like domain / steroid Delta-isomerase activity / SnoaL-like domain / steroid metabolic process / NTF2-like domain superfamily / EQUILENIN / Steroid Delta-isomerase
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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 16, 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
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7498
Polymers29,0972
Non-polymers6526
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-48 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.907, 73.724, 95.727
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-EQU / EQUILENIN


Mass: 266.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / 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


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion / 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: 1.32→35.91 Å / Num. obs: 58753 / % possible obs: 97.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 13.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.033 / Rrim(I) all: 0.074 / Net I/σ(I): 12.4 / Num. measured all: 286924 / Scaling rejects: 80
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.32-1.344.91.4461373728290.430.721.621195.2
7.23-35.914.50.02419694380.9990.0130.0275099.2

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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: 1.32→32.2914 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.73
RfactorNum. reflection% reflection
Rfree0.1738 2894 4.93 %
Rwork0.1444 --
obs0.1459 58644 96.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.96 Å2 / Biso mean: 19.4081 Å2 / Biso min: 5.25 Å2
Refinement stepCycle: final / Resolution: 1.32→32.2914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 152 261 2388
Biso mean--21.7 31.61 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095112
X-RAY DIFFRACTIONf_angle_d1.0576889
X-RAY DIFFRACTIONf_chiral_restr0.074735
X-RAY DIFFRACTIONf_plane_restr0.007897
X-RAY DIFFRACTIONf_dihedral_angle_d14.7391853
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3204-1.3420.33231370.3078254994
1.342-1.36520.29521310.2612255695
1.3652-1.390.26851350.2489263396
1.39-1.41670.27941450.2375248993
1.4167-1.44570.26191440.2214252093
1.4457-1.47710.25511320.2048261497
1.4771-1.51150.22271370.1833262197
1.5115-1.54930.19691310.1689264897
1.5493-1.59110.1951290.1558261797
1.5911-1.6380.15621350.1469267497
1.638-1.69080.20391410.1414262498
1.6908-1.75130.17051340.1365266498
1.7513-1.82140.16011300.1296257294
1.8214-1.90430.16131500.1245267898
1.9043-2.00460.15151430.119270098
2.0046-2.13020.16021370.1172271199
2.1302-2.29460.13591260.1116272799
2.2946-2.52550.15181310.121270598
2.5255-2.89070.16811390.1288272098
2.8907-3.64120.15291560.1354279799
3.6412-32.29140.17161510.1515293199

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