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- PDB-1bit: THE CRYSTAL STRUCTURE OF ANIONIC SALMON TRYPSIN IN A SECOND CRYST... -

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Basic information

Entry
Database: PDB / ID: 1bit
TitleTHE CRYSTAL STRUCTURE OF ANIONIC SALMON TRYPSIN IN A SECOND CRYSTAL FORM
ComponentsTRYPSIN
KeywordsSERINE PROTEINASE
Function / homology
Function and homology information


trypsin / digestion / serine-type endopeptidase activity / proteolysis / extracellular region / 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
BENZAMIDINE / : / Trypsin-1
Similarity search - Component
Biological speciesSalmo salar (Atlantic salmon)
MethodX-RAY DIFFRACTION / Resolution: 1.83 Å
AuthorsBerglund, G.I.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of anionic salmon trypsin in a second crystal form.
Authors: Berglund, G.I. / Smalas, A.O. / Hordvik, A. / Willassen, N.P.
#1: Journal: To be Published
Title: Cold-Adaption of Enzymes: Structural Comparison between Salmon and Bovine Trypsins
Authors: Smalas, A.O. / Heimstad, E.S. / Hordvik, A. / Willassen, N.P.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Crystal Structure Determination and Refinement of Benzamidine-Inhibited Trypsin from the North Atlantic Salmon (Salmo Salar)
Authors: Smalas, A.O. / Hordvik, A.
#3: 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.
#4: Journal: J.Mol.Biol. / Year: 1989
Title: Crystal Structure of Bovine B-Trypsin at 1.5 Angstroms Resolution in a Crystal Form with Low Molecular Packing Density
Authors: Bartunik, H.D. / Summers, L.J. / Bartsch, H.H.
#5: 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.
#6: 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.H. / Stroud, R.M.
History
DepositionAug 26, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Refinement description
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification

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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)25,7795
Polymers25,4031
Non-polymers3764
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.090, 82.330, 31.160
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: 25402.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmo salar (Atlantic salmon) / References: PIR: S31776, UniProt: P35031*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCALCIUM (IDENTIFIER CA) IS STRUCTURALLY BOUND IN THE SAME SEQUENTIAL POSITION AS FOR BOVINE TRYPSIN. ...CALCIUM (IDENTIFIER CA) IS STRUCTURALLY BOUND IN THE SAME SEQUENTIAL POSITION AS FOR BOVINE TRYPSIN. A SULFATE ION HAS BEEN LOCATED AT THE ACTIVE SITE REGION IN A SIMILAR POSITION REPORTED FOR BOVINE TRYPSIN.
Sequence detailsTHE AMINO ACID NUMBERING SYSTEM IS THE ONE ADOPTED FROM CHYMOTRYPSINOGEN AND IS ALSO THE SAME AS ...THE AMINO ACID NUMBERING SYSTEM IS THE ONE ADOPTED FROM CHYMOTRYPSINOGEN AND IS ALSO THE SAME AS USED FOR ALL THE PDB ENTRIES OF TRYPSINS FROM OTHER SPECIES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.78 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
20.7 Mammonium sulfate1reservoir
310 mM1reservoirCaCl2
460 mMbenzamidine1reservoir
550 mMsodium citrate-phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.83 Å / Num. obs: 15984 / % possible obs: 88.2 % / Num. measured all: 25917 / Rmerge F obs: 0.06

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.83→8 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.199 -
obs0.199 14271
Refinement stepCycle: LAST / Resolution: 1.83→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 24 125 1811
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
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
Software
*PLUS
Name: X-PLOR/PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.199 / Rfactor Rfree: 0.272
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.030.035
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_planar_d0.040.049
X-RAY DIFFRACTIONp_plane_restr0.020.015
X-RAY DIFFRACTIONp_chiral_restr0.060.053
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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