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- PDB-3sed: Crystal Structure of Ketosteroid Isomerase Variant M105A from Pse... -

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Basic information

Entry
Database: PDB / ID: 3sed
TitleCrystal Structure of Ketosteroid Isomerase Variant M105A from Pseudomonos putida
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE / Cysteine Sulfinic
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
Steroid Delta-isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.302 Å
AuthorsSomarowthu, S. / Brodkin, H.R. / D'Aquino, J.A. / Ringe, D. / Ondrechen, M.J. / Beuning, P.J.
CitationJournal: Biochemistry / Year: 2011
Title: A tale of two isomerases: compact versus extended active sites in ketosteroid isomerase and phosphoglucose isomerase.
Authors: Somarowthu, S. / Brodkin, H.R. / D'Aquino, J.A. / Ringe, D. / Ondrechen, M.J. / Beuning, P.J.
History
DepositionJun 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Feb 14, 2018Group: Advisory / Database references / Category: pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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


Theoretical massNumber of molelcules
Total (without water)13,7641
Polymers13,7641
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Steroid Delta-isomerase

A: Steroid Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)27,5272
Polymers27,5272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2050 Å2
ΔGint-11 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.080, 94.978, 72.286
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-134-

HOH

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Components

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


Mass: 13763.528 Da / Num. of mol.: 1 / Fragment: unp residues 3-127 / Mutation: M105A
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(DE3) / References: UniProt: P07445, steroid Delta-isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.4 M Ammonium sulfate 6.5% Isopropyl alcohol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 21, 2010
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.3→22.6 Å / Num. obs: 26517 / Redundancy: 5.8 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 1.5
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1923

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1OHO

1oho


Resolution: 1.302→22.559 Å / SU ML: 0.16 / σ(F): 0 / Phase error: 23.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 1871 7.63 %
Rwork0.2089 --
obs0.2106 24534 81.74 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.765 Å2 / ksol: 0.465 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--23.4282 Å20 Å2-0 Å2
2--5.5465 Å20 Å2
3----5.3044 Å2
Refinement stepCycle: LAST / Resolution: 1.302→22.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 0 39 990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008976
X-RAY DIFFRACTIONf_angle_d1.071327
X-RAY DIFFRACTIONf_dihedral_angle_d16.57363
X-RAY DIFFRACTIONf_chiral_restr0.065146
X-RAY DIFFRACTIONf_plane_restr0.007178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3022-1.33740.4314810.36591017X-RAY DIFFRACTION48
1.3374-1.37680.36811020.32231168X-RAY DIFFRACTION57
1.3768-1.42120.36661170.26221361X-RAY DIFFRACTION65
1.4212-1.4720.26321250.25331577X-RAY DIFFRACTION74
1.472-1.53090.24981500.19311728X-RAY DIFFRACTION82
1.5309-1.60060.22191540.17461907X-RAY DIFFRACTION90
1.6006-1.6850.20341660.16541972X-RAY DIFFRACTION94
1.685-1.79050.20021690.17052045X-RAY DIFFRACTION97
1.7905-1.92870.20471680.16652055X-RAY DIFFRACTION97
1.9287-2.12260.18621710.18072097X-RAY DIFFRACTION97
2.1226-2.42940.20121650.19342007X-RAY DIFFRACTION93
2.4294-3.05960.24821540.23151914X-RAY DIFFRACTION88
3.0596-22.5620.24411490.22391815X-RAY DIFFRACTION80

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