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- PDB-1mbq: Anionic Trypsin from Pacific Chum Salmon -

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Basic information

Entry
Database: PDB / ID: 1mbq
TitleAnionic Trypsin from Pacific Chum Salmon
ComponentsTrypsin
KeywordsHYDROLASE / psychrophilic enzymes / proteinase-catalyzed peptide coupling
Function / homology
Function and homology information


digestion / serine-type endopeptidase activity / proteolysis / extracellular region / 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 / Anionic trypsin
Similarity search - Component
Biological speciesOncorhynchus keta (chum salmon)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsToyota, E. / Ng, K.K.S. / Kuninaga, S. / Sekizaki, H. / Itoh, K. / Tanizawa, K. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal Structure and Nucleotide Sequence of an Anionic Trypsin from Chum Salmon (Oncorhynchus keta) in Comparison with Atlantic Salmon (Salmo salar) and Bovine Trypsin
Authors: Toyota, E. / Ng, K.K.S. / Kuninaga, S. / Sekizaki, H. / Itoh, K. / Tanizawa, K. / James, M.N.G.
History
DepositionAug 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7643
Polymers23,6041
Non-polymers1602
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.930, 48.010, 82.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Trypsin /


Mass: 23603.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oncorhynchus keta (chum salmon) / Organ: pyloric caeca / References: UniProt: Q8AV11, trypsin
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.89 Å3/Da / Density % sol: 35.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.15
Details: magnesium sulfate, Tris, calcium chloride, Tris-Cl, benzamidine, pH 8.15, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.62 mMCST1drop
230 mM1dropMgSO4
30.6 mM1dropCaCl2
46.0 mMbenzamidine1drop
550 mMTris-HCl1droppH8.15
61.4 M1reservoirMgSO4
70.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE DIP100 / Detector: IMAGE PLATE / Date: Jul 30, 1999 / Details: double-focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 17253 / Num. obs: 17253 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.31 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.25 % / Rmerge(I) obs: 0.183 / Rsym value: 0.183 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 108688
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2TBS

2tbs


Resolution: 1.8→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1708 -random
Rwork0.166 ---
all0.169 17234 --
obs0.169 17234 99.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.572 Å20 Å2-
2---0 Å2
3----0.114 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 10 91 1748
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_mcbond_it1.0241.5
X-RAY DIFFRACTIONc_mcangle_it1.9912
X-RAY DIFFRACTIONc_scbond_it1.5182
X-RAY DIFFRACTIONc_scangle_it2.8542.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5ben.paramben.top
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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