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- PDB-5dre: Crystal Structure of Ketosteroid Isomerase D38GP39GD99N mutant fr... -

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Basic information

Entry
Database: PDB / ID: 5dre
TitleCrystal Structure of Ketosteroid Isomerase D38GP39GD99N mutant from Pseudomonas Testosteroni (tKSI)
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 domain / Nuclear transport factor 2 (NTF2) 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
Steroid Delta-isomerase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å
AuthorsLamba, V. / Yabukarski, F. / 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: 2016
Title: Evaluation of the Catalytic Contribution from a Positioned General Base in Ketosteroid Isomerase.
Authors: Lamba, V. / Yabukarski, F. / Pinney, M. / Herschlag, D.
History
DepositionSep 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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


Theoretical massNumber of molelcules
Total (without water)13,3131
Polymers13,3131
Non-polymers00
Water55831
1
A: Steroid Delta-isomerase

A: Steroid Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)26,6262
Polymers26,6262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1890 Å2
ΔGint-6 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.362, 60.362, 142.103
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 13313.019 Da / Num. of mol.: 1 / Mutation: D38G, P39G, D99N
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: Potassium Phosphate 40 mM, Ammonium Sulfate 0.6 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2015
RadiationMonochromator: Si(111) Side scattering bent cube-root I-beam single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→42.11 Å / Num. obs: 8865 / % possible obs: 99.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 12.89
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.01 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NXJ

3nxj


Resolution: 2.151→42.107 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / Phase error: 31.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 459 5.19 %Random selection
Rwork0.2212 ---
obs0.2236 8850 99.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.151→42.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms921 0 0 31 952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007937
X-RAY DIFFRACTIONf_angle_d0.961269
X-RAY DIFFRACTIONf_dihedral_angle_d14.341330
X-RAY DIFFRACTIONf_chiral_restr0.037144
X-RAY DIFFRACTIONf_plane_restr0.004169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.151-2.46220.33711590.2642681X-RAY DIFFRACTION99
2.4622-3.1020.3511520.25132755X-RAY DIFFRACTION99
3.102-42.11460.22391480.20262955X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6180.52170.32461.463-0.83030.7350.1150.2067-0.0408-0.273-0.2325-0.6577-0.07550.53530.00070.37920.03660.01530.44220.06270.4533-21.196310.3656-11.9088
20.7058-0.34070.25691.0436-0.99381.5806-0.06020.10950.0563-0.2006-0.27120.01770.12170.0974-0.00140.40740.0078-0.03420.36590.02210.3339-28.16382.0641-9.4046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 58 )
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 125 )

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