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- PDB-4i8k: Bovine trypsin at 0.85 resolution -

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Basic information

Entry
Database: PDB / ID: 4i8k
TitleBovine trypsin at 0.85 resolution
ComponentsCationic trypsin
KeywordsHYDROLASE / Serine protease
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
BENZAMIDINE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.85 Å
AuthorsDauter, Z. / Liebschner, D. / Dauter, M. / Brzuszkiewicz, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin.
Authors: Liebschner, D. / Dauter, M. / Brzuszkiewicz, A. / Dauter, Z.
History
DepositionDec 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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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)23,7696
Polymers23,3241
Non-polymers4445
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.210, 58.300, 66.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 5 types, 437 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: protein solution: 30 mg/ml trypsin, 5mg/ml benzamidine and 3 mM CaCl2 in a 30 mM HEPES buffer pH 7.0. Well solution: 20% PEG 8000, 200 mM (NH4)2SO4, 100 mM cacodylate buffer pH 6.5 and 15% ...Details: protein solution: 30 mg/ml trypsin, 5mg/ml benzamidine and 3 mM CaCl2 in a 30 mM HEPES buffer pH 7.0. Well solution: 20% PEG 8000, 200 mM (NH4)2SO4, 100 mM cacodylate buffer pH 6.5 and 15% glycerol. 1:1 ratio drops, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.6199 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 0.85→30 Å / Num. obs: 183359 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 39.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
SHELXrefinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
SHELXLrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.85→30 Å / Occupancy max: 1 / Occupancy min: 0.17 / Cross valid method: Rfree / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.111 -random
Rwork0.096 --
all0.097 --
obs-183359 -
Displacement parametersBiso max: 61.35 Å2 / Biso mean: 10.3712 Å2 / Biso min: 3.58 Å2
Refinement stepCycle: LAST / Resolution: 0.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 26 432 2087
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d2.3

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