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Basic information

Entry
Database: PDB / ID: 1ntp
TitleUSE OF THE NEUTRON DIFFRACTION H/D EXCHANGE TECHNIQUE TO DETERMINE THE CONFORMATIONAL DYNAMICS OF TRYPSIN
ComponentsBETA-TRYPSIN
KeywordsHYDROLASE (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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
PHOSPHORYLISOPROPANE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodNEUTRON DIFFRACTION / Resolution: 1.8 Å
AuthorsKossiakoff, A.A.
Citation
Journal: Basic Life Sci. / Year: 1984
Title: Use of the neutron diffraction--H/D exchange technique to determine the conformational dynamics of trypsin
Authors: Kossiakoff, A.A.
#1: Journal: Nature / Year: 1982
Title: Protein Dynamics Investigated by the Neutron Diffraction-Hydrogen Exchange Technique
Authors: Kossiakoff, A.A.
#2: Journal: Biochemistry / Year: 1981
Title: Direct Determination of the Protonation States of Aspartic Acid-102 and Histidine-57 in the Tetrahedral Intermediate of the Serine Proteases. Neutron Structure of Trypsin
Authors: Kossiakoff, A.A. / Spencer, S.A.
#3: Journal: Nature / Year: 1980
Title: Neutron Diffraction Identifies His 57 as the Catalytic Base in Trypsin
Authors: Kossiakoff, A.A. / Spencer, S.A.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1979
Title: The Accuracy of Refined Protein Structures, Comparison of Two Independently Refined Models of Bovine Trypsin
Authors: Chambers, J.L. / Stroud, R.M.
#5: 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.
#6: Journal: Proteases and Biological Control / Year: 1975
Title: Structure-Function Relationships in the Serine Proteases
Authors: Stroud, R.M. / Krieger, M. / Koeppeii, R.E. / Kossiakoff, A.A. / Chambers, J.L.
#7: Journal: Biochem.Biophys.Res.Commun. / Year: 1974
Title: Silver Ion Inhibition of Serine Proteases, Crystallographic Study of Silver-Trypsin
Authors: Chambers, J.L. / Christoph, G.G. / Krieger, M. / Kay, L. / Stroud, R.M.
#8: Journal: J.Mol.Biol. / Year: 1974
Title: The Structure of Bovine Trypsin,Electron Density Maps of the Inhibited Enzyme at 5 Angstroms and at 2.7 Angstroms Resolution
Authors: Stroud, R.M. / Kay, L.M. / Dickerson, R.E.
#9: 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.
#10: 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
DepositionSep 16, 1987Processing site: BNL
Revision 1.0Jan 16, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4672
Polymers23,3271
Non-polymers1401
Water00
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
Atom site foot note1: SEE REMARK 4.
2: AN OCCUPANCY OF 0.0 INDICATES THAT NO SIGNIFICANT ELECTRON DENSITY WAS FOUND IN THE FINAL FOURIER MAP.

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Components

#1: Protein BETA-TRYPSIN


Mass: 23327.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-ISP / PHOSPHORYLISOPROPANE


Mass: 140.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O4P
Has protein modificationY
Nonpolymer detailsTHE ENZYME IS INHIBITED BY A MONOISOPROPYLPHOSPHORYL DERIVATIVE. THE REFINED STRUCTURE IN THIS ...THE ENZYME IS INHIBITED BY A MONOISOPROPYLPHOSPHORYL DERIVATIVE. THE REFINED STRUCTURE IN THIS REGION LOOKS VERY MUCH LIKE THAT EXPECTED FOR THE TETRAHEDRAL INTERMEDIATE IN THE REACTION SEQUENCE. THE NE2 OF HIS 57 IS HYDROGEN-BONDED TO O1A OF THE ISP GROUP, WHICH CORRESPONDS TO THE LEAVING GROUP NITROGEN OF A SPECIFIC SUBSTRATE.

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION

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Data collection

RadiationScattering type: neutron
Radiation wavelengthRelative weight: 1

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Processing

RefinementRfactor Rwork: 0.187 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 14 0 3230
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONo_bond_d0.013
NEUTRON DIFFRACTIONo_bond_d_na
NEUTRON DIFFRACTIONo_bond_d_prot
NEUTRON DIFFRACTIONo_angle_d
NEUTRON DIFFRACTIONo_angle_d_na
NEUTRON DIFFRACTIONo_angle_d_prot
NEUTRON DIFFRACTIONo_angle_deg2.3
NEUTRON DIFFRACTIONo_angle_deg_na
NEUTRON DIFFRACTIONo_angle_deg_prot
NEUTRON DIFFRACTIONo_dihedral_angle_d
NEUTRON DIFFRACTIONo_dihedral_angle_d_na
NEUTRON DIFFRACTIONo_dihedral_angle_d_prot
NEUTRON DIFFRACTIONo_improper_angle_d
NEUTRON DIFFRACTIONo_improper_angle_d_na
NEUTRON DIFFRACTIONo_improper_angle_d_prot
NEUTRON DIFFRACTIONo_mcbond_it
NEUTRON DIFFRACTIONo_mcangle_it
NEUTRON DIFFRACTIONo_scbond_it
NEUTRON DIFFRACTIONo_scangle_it

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