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- PDB-2tbs: COLD-ADAPTION OF ENZYMES: STRUCTURAL COMPARISON BETWEEN SALMON AN... -

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Basic information

Entry
Database: PDB / ID: 2tbs
TitleCOLD-ADAPTION OF ENZYMES: STRUCTURAL COMPARISON BETWEEN SALMON AND BOVINE TRYPSINS
ComponentsTRYPSIN
KeywordsHYDROLASE(SERINE PROTEINASE)
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
BENZAMIDINE / Trypsin-1
Similarity search - Component
Biological speciesSalmo salar (Atlantic salmon)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSmalas, A.O.
Citation
Journal: Proteins / Year: 1994
Title: Cold adaption of enzymes: structural comparison between salmon and bovine trypsins.
Authors: Smalas, A.O. / Heimstad, E.S. / Hordvik, A. / Willassen, N.P. / Male, R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Crystallization and Preliminary X-Ray Crystallographic Studies of Benzamidine-Inhibited Trypsin from the North Atlantic Salmon (Salmo Salar)
Authors: Smalas, A.O. / Hordvik, A.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallization and Preliminary X-Ray Crystallographic Studies of Benzamidine-Inhibited Trypsin from the North Atlantic Salmon (Salmo Salar)
Authors: Smalas, A.O. / Hordvik, A. / Hansen, L.K. / Hough, E. / Jynge, K.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1983
Title: The Geometry of the Reactive Site and of the Peptide Groups in Trypsin, Trypsinogen and its Complexes with Inhibitors
Authors: Marquart, M. / Walter, J. / Deisenhofer, J. / Bode, W. / Huber, R.
History
DepositionJan 14, 1994Processing site: BNL
SupersessionApr 30, 1994ID: 1TBS
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9453
Polymers23,7851
Non-polymers1602
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.950, 84.330, 39.110
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


Mass: 23784.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmo salar (Atlantic salmon) / References: UniProt: P35031, 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


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE CALCIUM IS ION IS BOUND IN A MANNER SIMILAR TO THAT OBSERVED IN BOVINE TRYPSIN.
Sequence detailsTHE AMINO ACID NUMBERING SCHEME USED IS ADOPTED FROM CHYMOTRYPSINOGEN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal grow
*PLUS
Temperature: 28-30 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1dropd
20.8 Macetate1drop
320 %sat1drop(NH4)2SO4

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→6 Å / Num. reflection obs: 14474 / σ(F): 3
Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT METHODS, USING THE MERLOT-PACKAGE (FITZGERALD, P. (1988) J.APPL. CRYST., 21, 273-278), AND THE REFINED MODEL OF BOVINE TRYPSIN AS SEARCH ...Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT METHODS, USING THE MERLOT-PACKAGE (FITZGERALD, P. (1988) J.APPL. CRYST., 21, 273-278), AND THE REFINED MODEL OF BOVINE TRYPSIN AS SEARCH MODEL (PROTEIN DATA BANK, ENTRY 3PTB). THIS ENTRY WAS REFINED USING A NON-STANDARD SETTING FOR THE SPACE GROUP P 21 21 2. THE FOLLOWING SYMMETRY OPERATORS MUST BE USED TO GENERATE CRYSTALLOGRAPHICALLY RELATED MOLECULES. X, Y, Z -X, 1/2+Y, -Z 1/2+X, -Y, -Z 1/2-X, 1/2-Y, Z
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 10 164 1833
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.01
X-RAY DIFFRACTIONp_angle_d0.040.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.0420.12
X-RAY DIFFRACTIONp_singtor_nbd0.1720.5
X-RAY DIFFRACTIONp_multtor_nbd0.3210.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2210.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.13
X-RAY DIFFRACTIONp_staggered_tor15.215
X-RAY DIFFRACTIONp_orthonormal_tor27.620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS

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