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- PDB-1try: STRUCTURE OF INHIBITED TRYPSIN FROM FUSARIUM OXYSPORUM AT 1.55 AN... -

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Basic information

Entry
Database: PDB / ID: 1try
TitleSTRUCTURE OF INHIBITED TRYPSIN FROM FUSARIUM OXYSPORUM AT 1.55 ANGSTROMS
ComponentsTRYPSIN
KeywordsHYDROLASE (SERINE PROTEINASE)
Function / homology
Function and homology information


trypsin / serine-type endopeptidase activity / proteolysis / extracellular region
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
ISOPROPYL ALCOHOL / PHOSPHORYLISOPROPANE / Trypsin
Similarity search - Component
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.55 Å
AuthorsRypniewski, W.R. / Dambmann, C. / Von Der Osten, C. / Dauter, M. / Wilson, K.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of inhibited trypsin from Fusarium oxysporum at 1.55 A.
Authors: Rypniewski, W.R. / Dambmann, C. / von der Osten, C. / Dauter, M. / Wilson, K.S.
#1: Journal: Protein Eng. / Year: 1994
Title: Evolutionary Divergence and Conservation of Trypsin
Authors: Rypniewski, W.R. / Perrakis, A. / Vorgias, C.E. / Wilson, K.S.
#2: Journal: Protein Eng. / Year: 1993
Title: The Sequence and X-Ray Structure of the Trypsin from Fusarium Oxysporum
Authors: Rypniewski, W.R. / Hastrup, S. / Betzel, Ch. / Dauter, M. / Dauter, Z. / Papendorf, G. / Branner, S. / Wilson, K.S.
History
DepositionMar 7, 1994Processing site: BNL
Revision 1.0Jan 1, 1996Provider: 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 1.4Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4013
Polymers22,2001
Non-polymers2002
Water7,206400
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.300, 67.890, 39.790
Angle α, β, γ (deg.)90.00, 107.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRYPSIN


Mass: 22200.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fusarium oxysporum (fungus) / References: UniProt: P35049, trypsin
#2: Chemical ChemComp-ISP / PHOSPHORYLISOPROPANE


Mass: 140.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O4P
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 1.93 Å3/Da / Density % sol: 36.37 %
Crystal
*PLUS
Density % sol: 36 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 5.5 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112.5 mg/mlprotein1drop
20.7 Mammonium sulfate1drop
350 mMcitrate1drop
41.4 Mammonium sulfate1reservoir
50.1 Msodium citrate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 10 Å / Num. obs: 23178 / % possible obs: 94.7 % / Num. measured all: 55012 / Rmerge(I) obs: 0.051 / Biso Wilson estimate: 22.4 Å2
Reflection shell
*PLUS
% possible obs: 69 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.55→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.144 23178
Refinement stepCycle: LAST / Resolution: 1.55→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 0 7 404 1981
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it2.133
X-RAY DIFFRACTIONo_mcangle_it2.864
X-RAY DIFFRACTIONo_scbond_it3.864
X-RAY DIFFRACTIONo_scangle_it5.325
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.0170.02
X-RAY DIFFRACTIONo_angle_d0.0390.04
X-RAY DIFFRACTIONo_dihedral_angle_d0.0480.05
X-RAY DIFFRACTIONo_plane_restr0.0150.02
X-RAY DIFFRACTIONo_chiral_restr0.1710.2

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