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- PDB-1may: BETA-TRYPSIN PHOSPHONATE INHIBITED -

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Basic information

Entry
Database: PDB / ID: 1may
TitleBETA-TRYPSIN PHOSPHONATE INHIBITED
ComponentsBETA-TRYPSIN
KeywordsHYDROLASE (SERINE PROTEASE) / HYDROLASE / SERINE PROTEASE / DIGESTION / PANCREAS / ZYMOGEN
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
Chem-ZAP / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsBertrand, J. / Oleksyszyn, J. / Kam, C. / Boduszek, B. / Presnell, S. / Plaskon, R. / Suddath, F. / Powers, J. / Williams, L.
Citation
Journal: Biochemistry / Year: 1996
Title: Inhibition of trypsin and thrombin by amino(4-amidinophenyl)methanephosphonate diphenyl ester derivatives: X-ray structures and molecular models.
Authors: Bertrand, J.A. / Oleksyszyn, J. / Kam, C.M. / Boduszek, B. / Presnell, S. / Plaskon, R.R. / Suddath, F.L. / Powers, J.C. / Williams, L.D.
#1: Journal: J.Mol.Biol. / Year: 1975
Title: The Refined Crystal Structure of Bovine Beta-Trypsin at 1.8 A Resolution
Authors: Bode, W. / Schwager, P.
History
DepositionFeb 6, 1996-
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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: BETA-TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7283
Polymers23,3241
Non-polymers4032
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.950, 58.550, 67.700
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: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PHOSPHONATE INHIBITED, TEMPERATURE 298 K / 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-ZAP / [N-(BENZYLOXYCARBONYL)AMINO](4-AMIDINOPHENYL)METHANE-PHOSPHONATE / Z-AMIDINOPHENYLMETHANE-PHOSPHONATE


Mass: 363.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N3O5P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE TRYPSIN RESIDUE NUMBERING USED IN THIS ENTRY IS BASED ON THE CHYMOTRYSINOGEN NUMBERING SYSTEM.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlbeta-trypsin1drop
25.0 mMMES1drop
31.0 mM1dropCaCl2
42.5 mMbenzamidine1drop
50.9 Mammonium sulfate1drop
65.0 mMMES1reservoir
71.0 mM1reservoirCaCl2
82.5 mMbenzamidine1reservoir
91.8 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jan 16, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 28987 / % possible obs: 96 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.12

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Processing

Software
NameVersionClassification
SANDIEGO MULTIWIREdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
SDMSdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.8→5 Å / σ(F): 0
Details: ATOMS C11 - C16 OF ZAP 195 HAVE OCCUPANCIES SET TO ZERO, AS DENSITY COULD NEVER BE LOCATED FOR THESE ATOMS DURING THE REFINEMENT. ATOMS C11 - C16 OF ZAP 195 HAVE OCCUPANCIES SET TO ZERO, AS ...Details: ATOMS C11 - C16 OF ZAP 195 HAVE OCCUPANCIES SET TO ZERO, AS DENSITY COULD NEVER BE LOCATED FOR THESE ATOMS DURING THE REFINEMENT. ATOMS C11 - C16 OF ZAP 195 HAVE OCCUPANCIES SET TO ZERO, AS DENSITY COULD NEVER BE LOCATED FOR THESE ATOMS DURING THE REFINEMENT.
RfactorNum. reflection
Rwork0.178 -
obs0.178 28987
Refinement stepCycle: LAST / Resolution: 1.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 25 89 1743
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.68
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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