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- PDB-7ry4: Multi-conformer model of Ketosteroid Isomerase Y57F/D40N mutant f... -

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Basic information

Entry
Database: PDB / ID: 7ry4
TitleMulti-conformer model of Ketosteroid Isomerase Y57F/D40N mutant from Pseudomonas Putida (pKSI) bound to a transition state analog 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 / Chem-J3Z / Steroid Delta-isomerase
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å
AuthorsYabukarski, F. / Doukov, T. / Herschlag, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1714723 United States
CitationJournal: Sci Adv / Year: 2022
Title: Ensemble-function relationships to dissect mechanisms of enzyme catalysis.
Authors: Yabukarski, F. / Doukov, T. / Pinney, M.M. / Biel, J.T. / Fraser, J.S. / Herschlag, D.
History
DepositionAug 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,82012
Polymers29,0632
Non-polymers75710
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-71 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.243, 74.554, 50.966
Angle α, β, γ (deg.)90.000, 110.701, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 14531.515 Da / Num. of mol.: 2 / Mutation: D40N, Y57F
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-CL / CHLORIDE ION


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


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-J3Z / (9beta,13alpha)-3-hydroxyestra-1,3,5(10)-trien-17-one / Estrone


Mass: 270.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 17-23% PEG 3350, 0.2 M MAGNESIUM CHLORIDE

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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: Feb 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.11→37.28 Å / Num. obs: 97398 / % possible obs: 97.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 12.23 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.044 / Net I/σ(I): 7.4
Reflection shellResolution: 1.11→1.13 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.764 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4738 / Rpim(I) all: 1.028 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U1Z

6u1z


Resolution: 1.11→29.37 Å / SU ML: 0.1169 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.9314
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1576 4893 5.04 %
Rwork0.1424 92272 -
obs0.1432 97165 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.52 Å2
Refinement stepCycle: LAST / Resolution: 1.11→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1985 0 48 249 2282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00846094
X-RAY DIFFRACTIONf_angle_d1.07058254
X-RAY DIFFRACTIONf_chiral_restr0.075885
X-RAY DIFFRACTIONf_plane_restr0.00741087
X-RAY DIFFRACTIONf_dihedral_angle_d14.47892228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.11-1.120.32361550.31612827X-RAY DIFFRACTION91.5
1.12-1.140.29561720.30663065X-RAY DIFFRACTION95.97
1.14-1.150.28311710.28152965X-RAY DIFFRACTION95.84
1.15-1.160.31821480.27583100X-RAY DIFFRACTION96.7
1.16-1.180.27821830.26222986X-RAY DIFFRACTION96.82
1.18-1.20.25341720.25583014X-RAY DIFFRACTION97.34
1.2-1.210.2681530.25253073X-RAY DIFFRACTION96.3
1.21-1.230.25781550.24453013X-RAY DIFFRACTION96.76
1.23-1.250.26231460.24673083X-RAY DIFFRACTION95.17
1.25-1.270.23811400.21843060X-RAY DIFFRACTION97.65
1.27-1.290.23451520.20583114X-RAY DIFFRACTION98.08
1.29-1.320.2161460.19823104X-RAY DIFFRACTION98.37
1.32-1.340.23981600.19023128X-RAY DIFFRACTION98.33
1.34-1.370.21091600.17683061X-RAY DIFFRACTION98.29
1.37-1.40.19331730.16733093X-RAY DIFFRACTION98.79
1.4-1.430.19341650.15323096X-RAY DIFFRACTION98.43
1.43-1.470.18081590.14273109X-RAY DIFFRACTION98.73
1.47-1.510.15371570.12893116X-RAY DIFFRACTION96.38
1.51-1.550.15361500.11662949X-RAY DIFFRACTION94.92
1.55-1.60.14091680.10973114X-RAY DIFFRACTION99
1.6-1.660.12611700.10763131X-RAY DIFFRACTION99.13
1.66-1.720.12691630.11033118X-RAY DIFFRACTION99.15
1.72-1.80.1231650.10823153X-RAY DIFFRACTION99.25
1.8-1.90.13111570.10733126X-RAY DIFFRACTION99.03
1.9-2.020.13671650.1083132X-RAY DIFFRACTION98.71
2.02-2.170.131630.11012987X-RAY DIFFRACTION95.51
2.17-2.390.12741810.11053149X-RAY DIFFRACTION99.23
2.39-2.740.14931700.12193135X-RAY DIFFRACTION99.1
2.74-3.450.12911710.13423155X-RAY DIFFRACTION98.96
3.45-29.370.1462030.143116X-RAY DIFFRACTION97.91

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