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- PDB-1tec: CRYSTALLOGRAPHIC REFINEMENT BY INCORPORATION OF MOLECULAR DYNAMIC... -

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Basic information

Entry
Database: PDB / ID: 1tec
TitleCRYSTALLOGRAPHIC REFINEMENT BY INCORPORATION OF MOLECULAR DYNAMICS. THE THERMOSTABLE SERINE PROTEASE THERMITASE COMPLEXED WITH EGLIN-C
Components
  • EGLIN C
  • THERMITASE
KeywordsCOMPLEX(SERINE PROTEINASE-INHIBITOR)
Function / homology
Function and homology information


thermitase / serine-type endopeptidase inhibitor activity / response to wounding / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Thermitase-like, domain / Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / Peptidase S8/S53 domain / : / Peptidase S8, subtilisin, His-active site ...Thermitase-like, domain / Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / Peptidase S8/S53 domain / : / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Eglin C / Thermitase
Similarity search - Component
Biological speciesThermoactinomyces vulgaris (bacteria)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsGros, P. / Dijkstra, B.W. / Hol, W.G.J.
CitationJournal: Acta Crystallogr.,Sect.B / Year: 1989
Title: Crystallographic refinement by incorporation of molecular dynamics: thermostable serine protease thermitase complexed with eglin c.
Authors: Gros, P. / Fujinaga, M. / Dijkstra, B.W. / Kalk, K.H. / Hol, W.G.
History
DepositionMay 24, 1989Processing site: BNL
Revision 1.0Oct 15, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: THERMITASE
I: EGLIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5885
Polymers36,4852
Non-polymers1033
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-33 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.250, 72.100, 89.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES 172 IS A CIS PROLINE. / 2: THE BOND PRO 214 - THR 215 IS IN THE CIS CONFORMATION.

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Components

#1: Protein THERMITASE


Mass: 28384.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / References: UniProt: P04072, thermitase
#2: Protein EGLIN C


Mass: 8100.011 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / References: UniProt: P01051
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMbis-(2-hydroxyethyl)iminotris(hydroxylmethyl)methane1reservoir
215 %PEG60001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 16310 / Rmerge F obs: 0.05 / Num. measured all: 63206

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Processing

SoftwareName: GROMOS / Classification: refinement
RefinementHighest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 3 208 2737
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.02
X-RAY DIFFRACTIONo_angle_deg3.16
X-RAY DIFFRACTIONo_dihedral_angle_d26.1
Refinement
*PLUS
Lowest resolution: 6 Å / Highest resolution: 2.2 Å / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_improper_angle_d0.024
X-RAY DIFFRACTIONo_plane_restr0.058

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