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- PDB-1trn: CRYSTAL STRUCTURE OF HUMAN TRYPSIN 1: UNEXPECTED PHOSPHORYLATION ... -

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Basic information

Entry
Database: PDB / ID: 1trn
TitleCRYSTAL STRUCTURE OF HUMAN TRYPSIN 1: UNEXPECTED PHOSPHORYLATION OF TYROSINE 151
ComponentsTRYPSIN
KeywordsHYDROLASE (SERINE PROTEINASE) / HUMAN TRYPSIN / DFP INHIBITED
Function / homology
Function and homology information


Uptake of dietary cobalamins into enterocytes / Developmental Lineage of Pancreatic Acinar Cells / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / trypsin / digestion / : / blood microparticle / serine-type endopeptidase activity / proteolysis ...Uptake of dietary cobalamins into enterocytes / Developmental Lineage of Pancreatic Acinar Cells / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / trypsin / digestion / : / blood microparticle / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsGaboriaud, C. / Fontecilla-Camps, J.C.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: Crystal structure of human trypsin 1: unexpected phosphorylation of Tyr151.
Authors: Gaboriaud, C. / Serre, L. / Guy-Crotte, O. / Forest, E. / Fontecilla-Camps, J.C.
History
DepositionMar 16, 1995Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN
B: TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7154
Polymers48,4342
Non-polymers2802
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.120, 107.120, 39.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.683235, -0.730181, 0.005026), (-0.730173, -0.683252, -0.003589), (0.006055, -0.001218, -0.999981)
Vector: 2.4711, 75.8229, 24.0978)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 16 .. B 302 A 16 .. A 302 0.311

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Components

#1: Protein TRYPSIN


Mass: 24217.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P07477, trypsin
#2: Chemical ChemComp-ISP / PHOSPHORYLISOPROPANE


Mass: 140.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9O4P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
141 mg/mlprotein1drop
214-16 %PEG60001reservoir
32-3 %(v/v)dioxane1reservoir
450 mMTAPS1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1992
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionNum. obs: 22989 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.044
Reflection
*PLUS
Highest resolution: 2.18 Å / Lowest resolution: 10 Å / Num. measured all: 63716 / Rmerge(I) obs: 0.044 / Biso Wilson estimate: 30.6 Å2
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.23 Å / % possible obs: 91.7 %

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Processing

Software
NameClassification
MOSFLMdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.177 --
obs0.177 22613 97.6 %
Displacement parametersBiso mean: 32.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 22 301 3705
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.34
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2
X-RAY DIFFRACTIONx_improper_angle_deg2.1

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