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- PDB-3mi4: Bovine trypsin at 0.8 A resolution, non-restrained refinement -

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Basic information

Entry
Database: PDB / ID: 3mi4
TitleBovine trypsin at 0.8 A resolution, non-restrained refinement
ComponentsCationic trypsin
KeywordsHYDROLASE / Trypsin / serine proteinase
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 / AB INITIO PHASING / Resolution: 0.8 Å
AuthorsBrzuszkiewicz, A. / Dauter, M. / Dauter, Z.
CitationJournal: To be Published
Title: Bovine trypsin at 0.8 A and role of restraints at ultra-high resolution
Authors: Brzuszkiewicz, A. / Dauter, M. / Dauter, Z.
History
DepositionApr 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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)23,6735
Polymers23,3241
Non-polymers3484
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.220, 58.530, 66.450
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 / Alpha-trypsin chain 1 / Alpha-trypsin chain 2


Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: residues 24-246 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 5 types, 484 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.: 1 / 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.: 480 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution: 30 mg/ml, 5 mg/ml benzamidine, 3 mM CaCl2, 30 mM HEPES buffer pH 7.0. Well solution: 20% PEG8000, 200 mM Am2SO4, 100 mM cacodylate buffer pH 6.5, 15% glycerol. Protein and ...Details: Protein solution: 30 mg/ml, 5 mg/ml benzamidine, 3 mM CaCl2, 30 mM HEPES buffer pH 7.0. Well solution: 20% PEG8000, 200 mM Am2SO4, 100 mM cacodylate buffer pH 6.5, 15% glycerol. Protein and well solutions mixed 1:1, 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: 0.62 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2009 / Details: Mirrors
RadiationMonochromator: Si 111 Double / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.62 Å / Relative weight: 1
ReflectionResolution: 0.8→30 Å / Num. all: 220132 / Num. obs: 220132 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 5.8 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 24.7
Reflection shellResolution: 0.8→0.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 1.8 / Num. unique all: 21729 / Rsym value: 0.757 / % possible all: 99.3

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Processing

Software
NameClassification
ACORNphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1123 2204 1 %Random
Rwork0.105 ---
all0.105 220132 --
obs-176867 80.3 %-
Refinement stepCycle: LAST / Resolution: 0.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 21 480 2130
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.031
X-RAY DIFFRACTIONs_angle_d0.041

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