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- PDB-5ugi: Crystal Structure of Ketosteroid Isomerase D38GF54A mutant from P... -

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Basic information

Entry
Database: PDB / ID: 5ugi
TitleCrystal Structure of Ketosteroid Isomerase D38GF54A mutant from Pseudomonas Testosteroni (tKSI) bound to Equilenin
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE / Enzyme
Function / homology
Function and homology information


steroid Delta-isomerase / steroid Delta-isomerase activity / steroid metabolic process
Similarity search - Function
Steroid delta5-4-isomerase / Ketosteroid isomerase / Nuclear transport factor 2 (NTF2) domain / SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
EQUILENIN / Steroid Delta-isomerase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYabukarski, F. / Lamba, V. / Herschlag, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1121778 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: An Activator-Blocker Pair Provides a Controllable On-Off Switch for a Ketosteroid Isomerase Active Site Mutant.
Authors: Lamba, V. / Yabukarski, F. / Herschlag, D.
History
DepositionJan 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5442
Polymers13,2781
Non-polymers2661
Water1,44180
1
A: Steroid Delta-isomerase
hetero molecules

A: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0894
Polymers26,5562
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1990 Å2
ΔGint-7 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.777, 60.777, 143.087
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-352-

HOH

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Components

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


Mass: 13277.969 Da / Num. of mol.: 1 / Mutation: D38G, F54A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Gene: ksi / Production host: Escherichia coli (E. coli) / References: UniProt: P00947, steroid Delta-isomerase
#2: Chemical ChemComp-EQU / EQUILENIN


Mass: 266.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 40 mM Potassium Phosphate, 1.0 M Ammonium Sulfate, 0.25 M Trimethyl acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.8→35.34 Å / Num. obs: 15307 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 1 / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 12.3 % / Rmerge(I) obs: 2.688 / Mean I/σ(I) obs: 1 / CC1/2: 0.707 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(dev_2376: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NXJ

3nxj


Resolution: 1.8→35.34 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / Phase error: 24.08
RfactorNum. reflection% reflection
Rfree0.2268 793 5.21 %
Rwork0.1787 --
obs0.1813 15227 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→35.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms927 0 20 80 1027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051039
X-RAY DIFFRACTIONf_angle_d0.7241428
X-RAY DIFFRACTIONf_dihedral_angle_d10.577604
X-RAY DIFFRACTIONf_chiral_restr0.052159
X-RAY DIFFRACTIONf_plane_restr0.005188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8003-1.91310.31871310.25712336X-RAY DIFFRACTION99
1.9131-2.06080.29411360.17862326X-RAY DIFFRACTION100
2.0608-2.26810.25171120.14592376X-RAY DIFFRACTION100
2.2681-2.59620.21371420.15772364X-RAY DIFFRACTION100
2.5962-3.27060.24541430.18592421X-RAY DIFFRACTION100
3.2706-35.35010.20291290.18092611X-RAY DIFFRACTION100

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