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- PDB-2tec: MOLECULAR DYNAMICS REFINEMENT OF A THERMITASE-EGLIN-C COMPLEX AT ... -

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Entry
Database: PDB / ID: 2tec
TitleMOLECULAR DYNAMICS REFINEMENT OF A THERMITASE-EGLIN-C COMPLEX AT 1.98 ANGSTROMS RESOLUTION AND COMPARISON OF TWO CRYSTAL FORMS THAT DIFFER IN CALCIUM CONTENT
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 space / 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 / Serine proteases, subtilase family, histidine 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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / 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 speciesHirudinaria manillensis (invertebrata)
Thermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.98 Å
AuthorsGros, P. / Betzel, C. / Dauter, Z. / Wilson, K.S. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 1989
Title: Molecular dynamics refinement of a thermitase-eglin-c complex at 1.98 A resolution and comparison of two crystal forms that differ in calcium content.
Authors: Gros, P. / Betzel, C. / Dauter, Z. / Wilson, K.S. / Hol, W.G.
History
DepositionOct 26, 1990Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 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_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

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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)36,6055
Polymers36,4852
Non-polymers1203
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-33 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.060, 67.230, 90.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE PRO E 172 IS A CIS PROLINE.
2: THE BOND PRO E 214 - THR E 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 natural source / Source: (natural) 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.) Hirudinaria manillensis (invertebrata) / Production host: unidentified (others) / References: UniProt: P01051
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERMITASE RESIDUE 199 IS A VALINE ACCORDING TO AMINO ACID SEQUENCE DETERMINATION BY MELOUN ET AL. ...THERMITASE RESIDUE 199 IS A VALINE ACCORDING TO AMINO ACID SEQUENCE DETERMINATION BY MELOUN ET AL. (FEBS LETT. V. 183, P. 195-199), BUT THE ELECTRON DENSITY SHOWS A TRYPTOPHAN. HOWEVER A TRP HAS NOT BEEN MODELLED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal grow
*PLUS
Temperature: 19-21 ℃ / pH: 5.2 / Method: vapor diffusion, hanging drop / Details: half of the reservoirs contained 0.5 M NaCl
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlthermitase1drop
21.7 mg/mleglin c1drop
337.5 mMsodium acetate1drop
45 mM1dropCaCl2
55 %PEG40001drop
68-22 %PEG40001reservoir
70.5 M1reservoirNaCl

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 3.5 Å / Num. obs: 26664 / % possible obs: 93 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.072 / Num. measured all: 94298

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Processing

SoftwareName: GROMOS / Classification: refinement
RefinementRfactor Rwork: 0.165 / Highest resolution: 1.98 Å
Refinement stepCycle: LAST / Highest resolution: 1.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 3 224 2753
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.019
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_deg2.73
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d16.77
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_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 1.98 Å / Rfactor obs: 0.165 / Lowest resolution: 8 Å / Num. reflection obs: 19730 / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_plane_restr0.047

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