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- PDB-2g8t: Indole-amidine Complexes with Bovine Trypsin -

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Basic information

Entry
Database: PDB / ID: 2g8t
TitleIndole-amidine Complexes with Bovine Trypsin
ComponentsCationic trypsin
KeywordsHYDROLASE / Trypsin amidine indole inhibition
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
2-(2-METHYLPHENYL)-1H-INDOLE-5-CARBOXIMIDAMIDE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsKline, A.D. / Briggs, S.L. / Subramaniam, S.
CitationJournal: To be published
Title: Ligand Epitoping By Proton NMR Chemical Shift Differences
Authors: Kline, A.D. / Briggs, S.L. / Subramaniam, S.
History
DepositionMar 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7104
Polymers23,3241
Non-polymers3853
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.525, 54.525, 107.807
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#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) / Organ: Pancreas / 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MI2 / 2-(2-METHYLPHENYL)-1H-INDOLE-5-CARBOXIMIDAMIDE


Mass: 249.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 1.98 Å3/Da / Density % sol: 37.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Trypsin, final concentration of 0.6 mM, was dissolved in 20 mM HEPES pH 7.0, 10 mM calcium chloride, 3% DMSO, and 3 mM of ligand of interest (compounds 3, 6, and 9). The well solution ...Details: Trypsin, final concentration of 0.6 mM, was dissolved in 20 mM HEPES pH 7.0, 10 mM calcium chloride, 3% DMSO, and 3 mM of ligand of interest (compounds 3, 6, and 9). The well solution consisted of 100 mM Cacodylate pH 6.5, 200 mM ammonium sulfate, 50% PEG (17% to 28%). The ligands were co crystallized with protein using vapor diffusion and hanging drop method. The drops were 1:1 (protein:well solution) and the plates were stored at 20 degrees centigrade. The crystals were generally present within two days. The cryo-protectant consisted of adding 75 l of an adjusted well solution, adjusted with PEG 8000 to 0.5% higher, and 25 l of glycerol. drop 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 17, 2005 / Details: Mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.41→43.25 Å / Num. all: 36557 / Num. obs: 36505 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 4 / Biso Wilson estimate: 13.9 Å2
Reflection shellResolution: 1.41→1.5 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNX2002refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→43.25 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2611570.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 3644 10 %RANDOM
Rwork0.19 ---
all0.191 36557 --
obs0.191 36505 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.0715 Å2 / ksol: 0.381246 e/Å3
Displacement parametersBiso mean: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.28 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-50 Å
Luzzati sigma a0.09 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.41→43.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 25 298 1955
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.91.5
X-RAY DIFFRACTIONc_mcangle_it1.382
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.562.5
LS refinement shellResolution: 1.41→1.5 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.226 576 9.7 %
Rwork0.212 5360 -
obs-5360 99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.pprotein.top
X-RAY DIFFRACTION2inh.top
X-RAY DIFFRACTION3water_rep.parwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5inh.parinh.top

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