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- PDB-1utm: Trypsin specificity as elucidated by LIE calculations, X-ray stru... -

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Basic information

Entry
Database: PDB / ID: 1utm
TitleTrypsin specificity as elucidated by LIE calculations, X-ray structures and association constant measurements
ComponentsTRYPSIN I
KeywordsHYDROLASE / TRYPSIN / INHIBITOR SPECIFICITY / ELECTROSTATIC INTERACTIONS / COLD-ADAPTATION / MOLECULAR DYNAMICS / BINDING FREE ENERGY
Function / homology
Function and homology information


trypsin / digestion / 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
2-PHENYLETHYLAMINE / Trypsin-1
Similarity search - Component
Biological speciesSALMO SALAR (Atlantic salmon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.5 Å
AuthorsLeiros, H.-K.S. / Brandsdal, B.O. / Andersen, O.A. / Os, V. / Leiros, I. / Helland, R. / Otlewski, J. / Willassen, N.P. / Smalas, A.O.
CitationJournal: Protein Sci. / Year: 2004
Title: Trypsin Specificity as Elucidated by Lie Calculations, X-Ray Structures, and Association Constant Measurements
Authors: Leiros, H.-K.S. / Brandsdal, B.O. / Andersen, O.A. / Os, V. / Leiros, I. / Helland, R. / Otlewski, J. / Willassen, N.P. / Smalas, A.O.
History
DepositionDec 9, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2004Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1613
Polymers25,9981
Non-polymers1622
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.941, 85.085, 32.185
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein TRYPSIN I


Mass: 25998.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SALMO SALAR (Atlantic salmon) / Organ: PYLORIC CAECA / References: UniProt: P35031, trypsin
#2: Chemical ChemComp-PEA / 2-PHENYLETHYLAMINE


Mass: 122.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.67 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Temperature: 37 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.7 Mammonium sulfate1reservoir
210 mM1reservoirCaCl2
350 mMsodium citrate-phosphate1reservoirpH6.0
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.5→8 Å / Num. obs: 32883 / % possible obs: 97.9 % / Redundancy: 3.39 % / Biso Wilson estimate: 14.25 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.1
Reflection shellRmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.8 / % possible all: 93.4
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. measured all: 111508 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 93.4 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.217 -7 %RANDOM
Rwork0.189 ---
obs0.189 32682 97.9 %-
Displacement parametersBiso mean: 15.68 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 10 109 1785
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.756
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
Highest resolution: 1.5 Å / Lowest resolution: 8 Å / % reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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