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- PDB-7rxf: Multi-conformer model of Apo Ketosteroid Isomerase Y57F mutant fr... -

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Basic information

Entry
Database: PDB / ID: 7rxf
TitleMulti-conformer model of Apo Ketosteroid Isomerase 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: 1.16 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,1856
Polymers29,0652
Non-polymers1204
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-46 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.993, 74.139, 95.641
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: 14532.501 Da / Num. of mol.: 2 / Mutation: 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.: 215 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
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: Nov 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.16→35.99 Å / Num. obs: 88770 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 15.25 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.039 / Net I/σ(I): 7.7
Reflection shellResolution: 1.16→1.18 Å / Redundancy: 6.4 % / Rmerge(I) obs: 2.851 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4193 / Rpim(I) all: 1.192 / % possible all: 97.8

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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: 1.16→32.38 Å / SU ML: 0.1363 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.3811
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1709 4393 4.98 %
Rwork0.152 83818 -
obs0.1529 88211 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.91 Å2
Refinement stepCycle: LAST / Resolution: 1.16→32.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 4 215 2183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00865068
X-RAY DIFFRACTIONf_angle_d1.01936832
X-RAY DIFFRACTIONf_chiral_restr0.0755739
X-RAY DIFFRACTIONf_plane_restr0.0069908
X-RAY DIFFRACTIONf_dihedral_angle_d15.26161851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.16-1.170.33831310.3462508X-RAY DIFFRACTION91.28
1.17-1.190.32881400.33112652X-RAY DIFFRACTION95.75
1.19-1.20.35861420.33622727X-RAY DIFFRACTION95.6
1.2-1.220.32521380.32222632X-RAY DIFFRACTION96.11
1.22-1.230.35611540.3072761X-RAY DIFFRACTION98.35
1.23-1.250.29011520.2912749X-RAY DIFFRACTION98.74
1.25-1.270.30981480.28352755X-RAY DIFFRACTION99.01
1.27-1.290.28641430.26312800X-RAY DIFFRACTION98.63
1.29-1.310.29261580.25162719X-RAY DIFFRACTION98.9
1.31-1.330.24321380.2392802X-RAY DIFFRACTION98.82
1.33-1.350.25811480.22522770X-RAY DIFFRACTION99.22
1.35-1.380.23121370.21182790X-RAY DIFFRACTION99.29
1.38-1.40.22121560.21032746X-RAY DIFFRACTION99.18
1.4-1.430.20631430.19732808X-RAY DIFFRACTION99.16
1.43-1.460.21771540.17932743X-RAY DIFFRACTION99.35
1.46-1.50.20191490.16092855X-RAY DIFFRACTION99.44
1.5-1.530.18791480.14682756X-RAY DIFFRACTION99.49
1.53-1.570.16551440.13942839X-RAY DIFFRACTION99.63
1.57-1.620.17191420.13952812X-RAY DIFFRACTION99.6
1.62-1.670.17091510.13022794X-RAY DIFFRACTION99.9
1.67-1.730.15751430.12852844X-RAY DIFFRACTION99.9
1.73-1.80.1531440.12222842X-RAY DIFFRACTION99.53
1.8-1.880.1431510.12522819X-RAY DIFFRACTION99.83
1.88-1.980.15571540.1252830X-RAY DIFFRACTION99.83
1.98-2.110.13821490.12152855X-RAY DIFFRACTION99.87
2.11-2.270.1371280.11922869X-RAY DIFFRACTION99.93
2.27-2.50.13811350.12572874X-RAY DIFFRACTION99.64
2.5-2.860.14311550.1382882X-RAY DIFFRACTION99.87
2.86-3.60.15031590.13772942X-RAY DIFFRACTION100
3.6-32.380.16651590.14953043X-RAY DIFFRACTION99.38

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