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

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Basic information

Entry
Database: PDB / ID: 2pzv
TitleCrystal Structure of Ketosteroid Isomerase D40N from Pseudomonas Putida (pksi) with bound Phenol
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE / transition state analog bound
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
PHENOL / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPseudomonas putida (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsPybus, B. / Caaveiro, J.M.M. / Petsko, G.A. / Ringe, D.
CitationJournal: PLoS Biol. / Year: 2006
Title: Testing Electrostatic complementarity in Enzyme Catalysis: Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole
Authors: Kraut, D.A. / Sigala, P.A. / Pybus, B. / Liu, C.W. / Ringe, D. / Petsko, G.A. / Herschlag, D.
History
DepositionMay 18, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionJun 12, 2007ID: 2B32
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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

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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
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5678
Polymers58,1904
Non-polymers3764
Water5,711317
1
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2834
Polymers29,0952
Non-polymers1882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-1 kcal/mol
Surface area11990 Å2
MethodPISA
2
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2834
Polymers29,0952
Non-polymers1882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-1 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.905, 50.540, 72.290
Angle α, β, γ (deg.)90.02, 89.98, 110.21
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 14547.515 Da / Num. of mol.: 4 / Mutation: D40N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (unknown) / Gene: ksi / Plasmid: pKK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (unknown) / Strain (production host): BL21 / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical
ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.4 M ammonium sulphate, 7% (v/v) 2-propanol, 40 mM potasium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 119468 / Num. obs: 111105 / % possible obs: 93 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.037
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.415

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→22.54 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.344 / SU ML: 0.044 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: hydrogens have been added in the riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.227 11094 10 %RANDOM
Rwork0.183 ---
obs0.188 110554 86.04 %-
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: 26.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0.03 Å20.11 Å2
2---0.19 Å20.09 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.25→22.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 28 322 4366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224158
X-RAY DIFFRACTIONr_angle_refined_deg2.0241.9445675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1575541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16424.049205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45315682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6721533
X-RAY DIFFRACTIONr_chiral_restr0.1390.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023273
X-RAY DIFFRACTIONr_nbd_refined0.2280.22071
X-RAY DIFFRACTIONr_nbtor_refined0.320.22928
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2334
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.232
X-RAY DIFFRACTIONr_mcbond_it2.8591.52636
X-RAY DIFFRACTIONr_mcangle_it3.94824162
X-RAY DIFFRACTIONr_scbond_it4.90131736
X-RAY DIFFRACTIONr_scangle_it6.7124.51494
X-RAY DIFFRACTIONr_rigid_bond_restr3.2134372
X-RAY DIFFRACTIONr_sphericity_free12.4463322
X-RAY DIFFRACTIONr_sphericity_bonded8.54234044
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 634 -
Rwork0.318 5696 -
obs-6330 66.63 %

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