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- PDB-1cse: THE HIGH-RESOLUTION X-RAY CRYSTAL STRUCTURE OF THE COMPLEX FORMED... -

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Basic information

Entry
Database: PDB / ID: 1cse
TitleTHE HIGH-RESOLUTION X-RAY CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN SUBTILISIN CARLSBERG AND EGLIN C, AN ELASTASE INHIBITOR FROM THE LEECH HIRUDO MEDICINALIS. STRUCTURAL ANALYSIS, SUBTILISIN STRUCTURE AND INTERFACE GEOMETRY
Components
  • EGLIN C
  • SUBTILISIN CARLSBERG
KeywordsCOMPLEX(SERINE PROTEINASE-INHIBITOR)
Function / homology
Function and homology information


subtilisin / serine-type endopeptidase inhibitor activity / response to wounding / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
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 / Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 ...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 / Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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
Subtilisin / Subtilisin Carlsberg / Eglin C
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / Resolution: 1.2 Å
AuthorsBode, W.
Citation
Journal: Eur.J.Biochem. / Year: 1987
Title: The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis. Structural analysis, ...Title: The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis. Structural analysis, subtilisin structure and interface geometry.
Authors: Bode, W. / Papamokos, E. / Musil, D.
#1: Journal: Embo J. / Year: 1986
Title: Refined 1.2 Angstroms Crystal Structure of the Complex Formed between Subtilisin Carlsberg and the Inhibitor Eglin C. Molecular Structure of Eglin and its Detailed Interaction with Subtilisin
Authors: Bode, W. / Papamokos, E. / Musil, D. / Seemueller, U. / Fritz, H.
#2: Journal: FEBS Lett. / Year: 1985
Title: Crystal and Molecular Structure of the Inhibitor Eglin from Leeches in Complex with Subtilisin Carlsberg
Authors: Mcphalen, C.A. / Schnebli, H.P. / James, M.N.G.
History
DepositionJun 3, 1988Processing site: BNL
Revision 1.0Jul 16, 1988Provider: 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 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _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: SUBTILISIN CARLSBERG
I: EGLIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4854
Polymers35,4052
Non-polymers802
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-20 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.300, 41.500, 57.000
Angle α, β, γ (deg.)111.80, 85.80, 104.70
Int Tables number1
Space group name H-MP1
Atom site foot note1: RESIDUE PRO 168 IS A CIS PROLINE. / 2: RESIDUE THR 211 IS A CIS THREONINE. / 3: SEE REMARK 3.

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Components

#1: Protein SUBTILISIN CARLSBERG


Mass: 27306.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
References: UniProt: P00780, UniProt: B0FXJ2*PLUS, subtilisin
#2: Protein EGLIN C


Mass: 8099.025 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop / Details: seeding
Components of the solutions
*PLUS
Conc.: 4-5 % / Common name: PEG

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Data collection

Reflection
*PLUS
Highest resolution: 1.2 Å / Num. obs: 46280 / % possible obs: 45 % / Num. measured all: 94661 / Rmerge(I) obs: 0.092

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 1.2→10 Å
Details: RESIDUE THR 211 IS A CIS THREONINE. IT WAS ORIGINALLY MODELLED AS A TRANS CONFORMER. AS OUTLINED IN REFERENCE 1 ABOVE, HOWEVER, THE MAIN CHAIN ANGLES OF THIS RESIDUE WERE OUTSIDE THE ALLOWED ...Details: RESIDUE THR 211 IS A CIS THREONINE. IT WAS ORIGINALLY MODELLED AS A TRANS CONFORMER. AS OUTLINED IN REFERENCE 1 ABOVE, HOWEVER, THE MAIN CHAIN ANGLES OF THIS RESIDUE WERE OUTSIDE THE ALLOWED REGIONS AND THE FIT TO THE ELECTRON DENSITY WAS STILL INSUFFICIENT. THE CIS CONFORMER GIVEN IN THIS ENTRY FITS MUCH BETTER. THE MODIFIED MODEL HAS BEEN SUBJECTED TO TWO FURTHER MINICYCLES OF POSITIONAL AND B FACTOR REFINEMENT WITHOUT GROSS CONFORMATION CHANGES AND WITHOUT AFFECTING THE R VALUE. TWO SITES PROBABLY OCCUPIED BY CALCIUM IONS AND 432 SOLVENT MOLECULES WERE LOCATED. FOR THESE 434 NON-PROTEIN ATOMS REFINED INDIVIDUAL OCCUPANCIES ARE GIVEN.
RfactorNum. reflection
Rwork0.178 -
obs-44500
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 2 432 2876
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.022
X-RAY DIFFRACTIONo_angle_deg2.48
Software
*PLUS
Name: EREF / Classification: refinement
Refinement
*PLUS
σ(F): 2 / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_d / Dev ideal: 2.48

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