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- PDB-1bty: Crystal structure of beta-trypsin in complex with benzamidine -

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Basic information

Entry
Database: PDB / ID: 1bty
TitleCrystal structure of beta-trypsin in complex with benzamidine
ComponentsBETA-TRYPSIN
KeywordsHYDROLASE / BENZAMIDINE INHIBITED / HYDROLASE (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 / Resolution: 1.5 Å
AuthorsStroud, R.M. / Katz, B.A. / Finer-Moore, J.
Citation
Journal: Biochemistry / Year: 1995
Title: Episelection: novel Ki approximately nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface.
Authors: Katz, B.A. / Finer-Moore, J. / Mortezaei, R. / Rich, D.H. / Stroud, R.M.
#1: Journal: Proteins: Struct.,Funct.,Genet. / Year: 1992
Title: Solvent Structure in Crystals of Trypsin Determined by X-Ray and Neutron Diffraction
Authors: Finer-Moore, J.S. / Kossiakoff, A. / Hurley, J.H. / Earnest, T. / Stroud, R.M.
#2: Journal: Proteins: Struct.,Funct.,Genet. / Year: 1991
Title: 1.59 Angstrom Structure of Trypsin at 120K: Comparison of Low Temperature and Room Temperature Structures
Authors: Earnest, T. / Fauman, E. / Craik, C.S. / Stroud, R.M.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1977
Title: Difference Fourier Refinement of the Structure of Dip-Trypsin at 1.5 Angstroms Using a Minicomputer Technique
Authors: Chambers, J.L. / Stroud, R.M.
#4: Journal: J.Mol.Biol. / Year: 1974
Title: Structure and Specific Binding of Trypsin, Comparison of Inhibited Derivatives and a Model for Substrate Binding
Authors: Krieger, M. / Kay, L.M. / Stroud, R.M.
#5: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: The Crystal and Molecular Structure of Dip-Inhibited Bovine Trypsin at 2.7 Angstroms Resolution
Authors: Stroud, R.M. / Kay, L.M. / Dickerson, R.E.
History
DepositionMay 17, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1733
Polymers24,0131
Non-polymers1602
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.840, 58.610, 67.470
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 BETA-TRYPSIN


Mass: 24012.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / 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-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.: 219 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal grow
*PLUS
pH: 8.15 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris11pH8.15
21.0 mg/mlbenzamidine11
3trypsin11150.0mg
4111.02gMgSO4-7H2O

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Data collection

DetectorDate: Aug 8, 1992
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 25157 / % possible obs: 69.2 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 8 Å

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Processing

Software
NameClassification
XDSdata scaling
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 1.5→8 Å / σ(F): 2.4 /
RfactorNum. reflection
Rwork0.161 -
obs0.161 24173
Refinement stepCycle: LAST / Resolution: 1.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 10 219 1858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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