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- PDB-4niw: Crystal structure of trypsiligase (K60E/N143H/Y151H/D189K trypsin... -

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Basic information

Entry
Database: PDB / ID: 4niw
TitleCrystal structure of trypsiligase (K60E/N143H/Y151H/D189K trypsin) orthorhombic form
ComponentsCationic trypsin
KeywordsHYDROLASE / Trypsin / Serine proteinase / Enzyme design / Activation domain / Zymogen / Peptide ligation / Reverse proteolysis
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.31 Å
AuthorsSchoepfel, M. / Parthier, C. / Stubbs, M.T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: N-terminal protein modification by substrate-activated reverse proteolysis.
Authors: Liebscher, S. / Schopfel, M. / Aumuller, T. / Sharkhuukhen, A. / Pech, A. / Hoss, E. / Parthier, C. / Jahreis, G. / Stubbs, M.T. / Bordusa, F.
History
DepositionNov 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4703
Polymers23,3371
Non-polymers1322
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.522, 58.607, 66.831
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cationic trypsin / Beta-trypsin / Alpha-trypsin chain 1 / Alpha-trypsin chain 2


Mass: 23337.330 Da / Num. of mol.: 1 / Fragment: UNP residues 24-246 / Mutation: K60E, N143H, Y151H, D189K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris/HCl, 0.2 M Li2SO4, 20% (w/v) polyethyleneglycol 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.31→44.064 Å / Num. obs: 51246 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 8.67 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.31-1.390.16610.8159955804296.5
1.39-1.480.12214.3257075763297.3
1.48-1.60.09318.3453414712897.5
1.6-1.760.07522.749443663498.3
1.76-1.960.06327.5244906605798.7
1.96-2.270.05631.9839487539399.1
2.27-2.770.05434.5833282460999.4
2.77-3.910.05136.6825761363599.7
3.910.05336.9114145211599.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→44.064 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.9353 / SU ML: 0.07 / σ(F): 2.03 / Phase error: 11.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1546 2562 5 %
Rwork0.1282 --
obs0.1296 51244 98.14 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.92 Å2 / Biso mean: 13.0581 Å2 / Biso min: 4.18 Å2
Refinement stepCycle: LAST / Resolution: 1.31→44.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 0 7 256 1878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051769
X-RAY DIFFRACTIONf_angle_d1.1722421
X-RAY DIFFRACTIONf_chiral_restr0.082276
X-RAY DIFFRACTIONf_plane_restr0.005311
X-RAY DIFFRACTIONf_dihedral_angle_d12.051657
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.31-1.33460.15661370.10772601273896
1.3346-1.36190.1331390.09412635277497
1.3619-1.39150.12631390.09462647278697
1.3915-1.42390.12671380.09182615275397
1.4239-1.45950.13751390.09382647278697
1.4595-1.49890.12151400.0912649278997
1.4989-1.5430.13681400.09192676281698
1.543-1.59290.1191400.09232661280198
1.5929-1.64980.13061410.09512679282098
1.6498-1.71580.13651430.09782704284798
1.7158-1.79390.15121410.10822693283499
1.7939-1.88850.13511430.11492705284898
1.8885-2.00680.15631440.11842739288399
2.0068-2.16180.151440.12452745288999
2.1618-2.37930.17321450.13632743288899
2.3793-2.72360.1771460.153927792925100
2.7236-3.43120.18561480.163728172965100
3.4312-44.08870.16091550.156929473102100

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