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- PDB-2inx: Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 2inx
TitleCrystal Structure of Ketosteroid Isomerase D40N from Pseudomonas putida (pKSI) with bound 2,6-difluorophenol
ComponentsSteroid delta-isomerase
KeywordsISOMERASE / KSI / enzyme / active site / charge distribution / hydrogen bond
Function / homology
Function and homology information


steroid Delta-isomerase / steroid Delta-isomerase activity / steroid metabolic process
Similarity search - Function
Ketosteroid isomerase / 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
2,6-DIFLUOROPHENOL / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMartinez Caaveiro, J.M. / Pybus, B. / Ringe, D. / Petsko, G.A. / Sigala, P. / Kraut, D. / Herschlag, D.
Citation
Journal: J.Am.Chem.Soc. / Year: 2008
Title: Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole.
Authors: Sigala, P.A. / Kraut, D.A. / Caaveiro, J.M. / Pybus, B. / Ruben, E.A. / Ringe, D. / Petsko, G.A. / Herschlag, D.
#1: Journal: PLOS Biol. / Year: 2006
Title: Testing Electrostatic Complementarity in Enzyme Catalysis: Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole
Authors: Kraut, D. / Sigala, P. / Pybus, B. / Liu, C.W. / Ringe, D. / Petsko, G.A. / Herschlag, D.
History
DepositionOct 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)14,6782
Polymers14,5481
Non-polymers1301
Water1,29772
1
A: Steroid delta-isomerase
hetero molecules

A: Steroid delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3554
Polymers29,0952
Non-polymers2602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)35.114, 94.887, 72.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-135-

HOH

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Components

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


Mass: 14547.515 Da / Num. of mol.: 1 / Mutation: D40N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical ChemComp-FFP / 2,6-DIFLUOROPHENOL


Mass: 130.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4F2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulphate 1.4 M, 2-propanol 6.5% protein concentration 25 mg/ml, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2004
RadiationMonochromator: Ge 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→47.4 Å / Num. all: 19911 / Num. obs: 19274 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.079 / Net I/σ(I): 16.1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 1890 / Rsym value: 0.374 / % possible all: 96.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B32

2b32
PDB Unreleased entry


Resolution: 1.5→47.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.648 / SU ML: 0.062 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1830 9.8 %RANDOM
Rwork0.185 ---
obs0.19 18650 93.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.929 Å2
Baniso -1Baniso -2Baniso -3
1-2.88 Å20 Å20 Å2
2---2.58 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.5→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 0 9 72 1101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221058
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.9451445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8745137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80823.44858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76815175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3331512
X-RAY DIFFRACTIONr_chiral_restr0.130.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02849
X-RAY DIFFRACTIONr_nbd_refined0.2190.2457
X-RAY DIFFRACTIONr_nbtor_refined0.3170.2723
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.211
X-RAY DIFFRACTIONr_mcbond_it2.2661.5661
X-RAY DIFFRACTIONr_mcangle_it3.28521036
X-RAY DIFFRACTIONr_scbond_it3.9573456
X-RAY DIFFRACTIONr_scangle_it5.54.5402
X-RAY DIFFRACTIONr_rigid_bond_restr2.57531117
X-RAY DIFFRACTIONr_sphericity_free11.133372
X-RAY DIFFRACTIONr_sphericity_bonded6.45231029
LS refinement shellResolution: 1.5→1.537 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 108 -
Rwork0.184 1150 -
obs-1258 85.93 %

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