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- PDB-1egq: ENHANCEMENT OF ENZYME ACTIVITY THROUGH THREE-PHASE PARTITIONING: ... -

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Basic information

Entry
Database: PDB / ID: 1egq
TitleENHANCEMENT OF ENZYME ACTIVITY THROUGH THREE-PHASE PARTITIONING: CRYSTAL STRUCTURE OF A MODIFIED SERINE PROTEINASE AT 1.5 A RESOLUTION
ComponentsPROTEINASE K
KeywordsHYDROLASE / Proteinase K / anhydrous organic solvents / stability / enhanced activity
Function / homology
Function and homology information


peptidase K / cellular anatomical entity / serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. ...Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Proteinase K
Similarity search - Component
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.55 Å
AuthorsSingh, R.K. / Gourinath, S. / Sharma, S. / Ray, I. / Gupta, M.N. / Singh, T.P.
CitationJournal: Protein Eng. / Year: 2001
Title: Enhancement of enzyme activity through three-phase partitioning: crystal structure of a modified serine proteinase at 1.5 A resolution.
Authors: Singh, R.K. / Gourinath, S. / Sharma, S. / Roy, I. / Gupta, M.N. / Betzel, C. / Srinivasan, A. / Singh, T.P.
History
DepositionFeb 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEINASE K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1315
Polymers28,9311
Non-polymers2004
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.290, 68.290, 106.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEINASE K /


Mass: 28930.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TRIPHASIC TREATED / Source: (natural) Engyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 6.5
Details: Sodium Nitrate, Calcium Chloride, Tris-HCl, pH 6.5, MICRODIALYSIS, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlenzyme11
250 mMTris-HCl11
31 mM11CaCl2
41 M12NaNO3

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→10 Å / Num. all: 240597 / Num. obs: 34371 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.7
Reflection shellResolution: 1.55→1.65 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.145 / Num. unique all: 4165 / % possible all: 75
Reflection
*PLUS
% possible obs: 96 % / Num. measured all: 240597
Reflection shell
*PLUS
% possible obs: 75 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementResolution: 1.55→10 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 783742.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2600 7.6 %RANDOM
Rwork0.193 ---
all0.197 ---
obs0.197 34371 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.26 Å2 / ksol: 0.417 e/Å3
Displacement parametersBiso mean: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2--0.54 Å20 Å2
3----1.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.55→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 10 243 2282
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 350 7.8 %
Rwork0.342 4165 -
obs--74.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CBM.PARAMCBM.TOP
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 7.6 % / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.7 Å2
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d

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