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- PDB-1cqs: CRYSTAL STRUCTURE OF D103E MUTANT WITH EQUILENINEOF KSI IN PSEUDO... -

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Basic information

Entry
Database: PDB / ID: 1cqs
TitleCRYSTAL STRUCTURE OF D103E MUTANT WITH EQUILENINEOF KSI IN PSEUDOMONAS PUTIDA
ComponentsPROTEIN : KETOSTEROID ISOMERASE
KeywordsISOMERASE / KSI / EQUILENIN / PUTIDA LBHB
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
EQUILENIN / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsChoi, G. / Ha, N.C. / Kim, S.W. / Kim, D.H. / Park, S. / Oh, B.H. / Choi, K.Y.
CitationJournal: Biochemistry / Year: 2000
Title: Asp-99 donates a hydrogen bond not to Tyr-14 but to the steroid directly in the catalytic mechanism of Delta 5-3-ketosteroid isomerase from Pseudomonas putida biotype B
Authors: Choi, G. / Ha, N.C. / Kim, S.W. / Kim, D.H. / Park, S. / Oh, B.H. / Choi, K.Y.
History
DepositionAug 11, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN : KETOSTEROID ISOMERASE
B: PROTEIN : KETOSTEROID ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6564
Polymers29,1232
Non-polymers5332
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-12 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.257, 72.081, 51.335
Angle α, β, γ (deg.)90.00, 90.94, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer of the asymmetric unit.

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Components

#1: Protein PROTEIN : KETOSTEROID ISOMERASE


Mass: 14561.542 Da / Num. of mol.: 2 / Fragment: KSI MUTANT / Mutation: D103E,D40N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical ChemComp-EQU / EQUILENIN


Mass: 266.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.83 Å3/Da / Density % sol: 56.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Sodium Acetate, Ammonium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
250 mMTris-Cl1droppH7.0
320 mMbeta-mercaptoethanol1drop
41.1 Mammonium acetate1reservoir
50.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Oct 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 25370 / Num. obs: 21961 / % possible obs: 86.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2 % / Rmerge(I) obs: 0.272 / Num. unique all: 1883 / % possible all: 75.1
Reflection
*PLUS
Highest resolution: 1.9 Å / Rmerge(I) obs: 0.046

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.843refinement
X-PLORphasing
RefinementResolution: 1.9→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1099 -RANDOM
Rwork0.204 ---
all0.204 25370 --
obs0.204 21971 5 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 40 76 2040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.79
X-RAY DIFFRACTIONx_bond_d0.016
Refinement
*PLUS
Highest resolution: 1.9 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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