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- PDB-3vgn: Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 3vgn
TitleCrystal Structure of Ketosteroid Isomerase D40N from Pseudomonas putida (pKSI) with bound 3-fluoro-4-nitrophenol
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE / hydrogen bond / KSI / enzyme catalysis / transition state / oxyanion hole
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
3-fluoro-4-nitrophenol / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsCaaveiro, J.M.M. / Pybus, B. / Ringe, D. / Petsko, G.A. / Sigala, P.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site
Authors: Sigala, P.A. / Fafarman, A.T. / Schwans, J.P. / Fried, S.D. / Fenn, T.D. / Caaveiro, J.M.M. / Pybus, B. / Ringe, D. / Petsko, G.A. / Boxer, S.G. / Herschlag, D.
History
DepositionAug 16, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,4094
Polymers29,0952
Non-polymers3142
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-11 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.483, 72.315, 95.282
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14547.515 Da / Num. of mol.: 2 / Mutation: D40N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical ChemComp-FNN / 3-fluoro-4-nitrophenol


Mass: 157.099 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4FNO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.1 Å3/Da / Density % sol: 41.45 % / Mosaicity: 0.965 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.4M Ammonium sulphate, 6-7% 2-propanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.82656 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 16, 2005
RadiationMonochromator: Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 1.3→35 Å / Num. all: 55738 / Num. obs: 55738 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.076 / Χ2: 1.006 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.353.70.73847001.003178.7
1.35-1.440.61550561.006183.8
1.4-1.464.10.47651671.008185.7
1.46-1.5440.33553111.008187.8
1.54-1.6440.23755051.012191.3
1.64-1.7640.1757821.006195.1
1.76-1.944.10.10758791.002196.8
1.94-2.224.30.07659881.005197.7
2.22-2.84.40.06160491.004197.9
2.8-354.20.0563011.005197.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.5 Å33.25 Å
Translation4.5 Å33.25 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FZW

3fzw


Resolution: 1.3→33.25 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.2498 / WRfactor Rwork: 0.1936 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.7999 / SU B: 2.252 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0635 / SU Rfree: 0.0631 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2814 5.1 %RANDOM
Rwork0.1694 ---
all0.1717 55738 --
obs0.1717 55689 91.21 %-
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 max: 106.63 Å2 / Biso mean: 22.6604 Å2 / Biso min: 9.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å20 Å2
2---0.07 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.3→33.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 22 171 2153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192281
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9483139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0815320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95823.906128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92815392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5831525
X-RAY DIFFRACTIONr_chiral_restr0.0940.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211867
X-RAY DIFFRACTIONr_rigid_bond_restr7.85532281
X-RAY DIFFRACTIONr_sphericity_free24.155533
X-RAY DIFFRACTIONr_sphericity_bonded14.30452341
LS refinement shellResolution: 1.301→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 181 -
Rwork0.268 3020 -
all-3201 -
obs--75.5 %

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