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- PDB-7rxk: Multi-conformer model of Apo Ketosteroid Isomerase Y32F/Y57F muta... -

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Basic information

Entry
Database: PDB / ID: 7rxk
TitleMulti-conformer model of Apo Ketosteroid Isomerase Y32F/Y57F mutant from Pseudomonas Putida (pKSI) 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 / Steroid Delta-isomerase
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 23, 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)29,1536
Polymers29,0332
Non-polymers1204
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-47 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.266, 74.059, 96.229
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 14516.501 Da / Num. of mol.: 2 / Mutation: Y32F, 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.73 %
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: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.1→37.03 Å / Num. obs: 105295 / % possible obs: 99.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 13.63 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.033 / Net I/σ(I): 9.2
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 6.3 % / Rmerge(I) obs: 2.86 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 5087 / Rpim(I) all: 1.233 / % possible all: 99

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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: 1.1→34.56 Å / SU ML: 0.1297 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1444
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1655 5233 5 %
Rwork0.1532 99509 -
obs0.1538 104742 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.76 Å2
Refinement stepCycle: LAST / Resolution: 1.1→34.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1987 0 4 271 2262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724921
X-RAY DIFFRACTIONf_angle_d0.95386596
X-RAY DIFFRACTIONf_chiral_restr0.0715730
X-RAY DIFFRACTIONf_plane_restr0.0063870
X-RAY DIFFRACTIONf_dihedral_angle_d14.18821804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.32591370.35733027X-RAY DIFFRACTION91.76
1.11-1.130.32221470.33623264X-RAY DIFFRACTION96.99
1.13-1.140.32041880.3183250X-RAY DIFFRACTION98.51
1.14-1.150.32031870.29763234X-RAY DIFFRACTION99.22
1.15-1.170.30721770.28443302X-RAY DIFFRACTION99.03
1.17-1.190.2951770.27873243X-RAY DIFFRACTION99.25
1.19-1.20.28631860.26273287X-RAY DIFFRACTION98.95
1.2-1.220.3011750.25173212X-RAY DIFFRACTION96.61
1.22-1.240.27481730.24163302X-RAY DIFFRACTION99.71
1.24-1.260.22251730.2253295X-RAY DIFFRACTION99.8
1.26-1.280.22611800.21833323X-RAY DIFFRACTION99.74
1.28-1.30.22431940.20723305X-RAY DIFFRACTION99.69
1.3-1.330.21561580.1983317X-RAY DIFFRACTION99.43
1.33-1.360.22461780.19463295X-RAY DIFFRACTION99.29
1.36-1.390.20481640.18253313X-RAY DIFFRACTION98.98
1.39-1.420.21511840.17423223X-RAY DIFFRACTION97.45
1.42-1.450.18721810.15473338X-RAY DIFFRACTION99.32
1.45-1.490.19221730.14273308X-RAY DIFFRACTION99.94
1.49-1.540.14581740.13093341X-RAY DIFFRACTION99.97
1.54-1.590.15771750.12593365X-RAY DIFFRACTION100
1.59-1.640.14181730.12453345X-RAY DIFFRACTION99.49
1.64-1.710.15911750.1253297X-RAY DIFFRACTION99.12
1.71-1.790.13481720.12313313X-RAY DIFFRACTION98.25
1.79-1.880.16041720.12153356X-RAY DIFFRACTION99.97
1.88-20.13381940.12223373X-RAY DIFFRACTION99.92
2-2.150.12821680.11643391X-RAY DIFFRACTION99.92
2.15-2.370.13911540.11973407X-RAY DIFFRACTION99.89
2.37-2.710.13131700.13143419X-RAY DIFFRACTION99.28
2.71-3.420.13811750.14183466X-RAY DIFFRACTION99.84
3.42-34.560.16041990.15983598X-RAY DIFFRACTION99.37

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