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- PDB-3cpo: Crystal structure of ketosteroid isomerase D40N with bound 2-fluo... -

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Basic information

Entry
Database: PDB / ID: 3cpo
TitleCrystal structure of ketosteroid isomerase D40N with bound 2-fluorophenol
ComponentsDelta(5)-3-ketosteroid isomerase
KeywordsISOMERASE / ENZYME / ACTIVE SITE / HYDROGEN BOND / GEOMETRY / Lipid metabolism / Steroid metabolism
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-fluorophenol / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.24 Å
AuthorsCaaveiro, J.M.M. / Pybus, B. / Ringe, D. / Petsko, G.
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.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.A. / Sigala, P.A. / Pybus, B. / Liu, C.W. / Ringe, D. / Petsko, G.A. / Herschlag, D.
History
DepositionMar 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
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
Revision 1.4Aug 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: Delta(5)-3-ketosteroid isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6602
Polymers14,5481
Non-polymers1121
Water1,26170
1
A: Delta(5)-3-ketosteroid isomerase
hetero molecules

A: Delta(5)-3-ketosteroid isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3194
Polymers29,0952
Non-polymers2242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2100 Å2
ΔGint-11.1 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.347, 95.013, 72.376
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-134-

HOH

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Components

#1: Protein Delta(5)-3-ketosteroid isomerase / Steroid Delta-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 / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical ChemComp-FP2 / 2-fluorophenol


Mass: 112.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5FO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: AMMONIUM SULPHATE 1.4 M, 2-PROPANOL 5-7%, PROTEIN CONCENTRATION 25 MG/ML, 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: BL9-1 / Wavelength: 0.97952 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 1.24→50 Å / Num. all: 33296 / Num. obs: 33296 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Rmerge(I) obs: 0.053 / Χ2: 1.006 / Net I/σ(I): 14.7
Reflection shellResolution: 1.24→1.28 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / Num. unique all: 2335 / Χ2: 1.006 / % possible all: 67.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.19 Å
Translation2.5 Å36.19 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2INX

2inx


Resolution: 1.24→36.19 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.591 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1669 5 %RANDOM
Rwork0.166 ---
all0.168 33253 --
obs0.168 33253 95.25 %-
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: 22.999 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2---1.29 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.24→36.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 0 8 73 1129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221094
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.9511506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.335151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17423.89859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37715191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8731511
X-RAY DIFFRACTIONr_chiral_restr0.1480.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02879
X-RAY DIFFRACTIONr_nbd_refined0.2330.6470
X-RAY DIFFRACTIONr_nbtor_refined0.3271745
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2121134
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.647
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.184123
X-RAY DIFFRACTIONr_mcbond_it3.8483679
X-RAY DIFFRACTIONr_mcangle_it4.92441078
X-RAY DIFFRACTIONr_scbond_it4.2523471
X-RAY DIFFRACTIONr_scangle_it5.3984411
X-RAY DIFFRACTIONr_rigid_bond_restr3.04931150
X-RAY DIFFRACTIONr_sphericity_free11.727373
X-RAY DIFFRACTIONr_sphericity_bonded8.45631056
LS refinement shellResolution: 1.24→1.274 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 94 -
Rwork0.287 1547 -
all-1641 -
obs--64.13 %

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