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- PDB-2sni: STRUCTURAL COMPARISON OF TWO SERINE PROTEINASE-PROTEIN INHIBITOR ... -

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Basic information

Entry
Database: PDB / ID: 2sni
TitleSTRUCTURAL COMPARISON OF TWO SERINE PROTEINASE-PROTEIN INHIBITOR COMPLEXES. EGLIN-C-SUBTILISIN CARLSBERG AND CI-2-SUBTILISIN NOVO
Components
  • CHYMOTRYPSIN INHIBITOR 2
  • SUBTILISIN NOVO
KeywordsCOMPLEX (PROTEINASE/INHIBITOR) / COMPLEX (PROTEINASE-INHIBITOR) / COMPLEX (PROTEINASE-INHIBITOR) complex
Function / homology
Function and homology information


subtilisin / sporulation resulting in formation of a cellular spore / fibrinolysis / 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. / : / Fervidolysin N-terminal prodomain / Trypsin Inhibitor V; Chain A / Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily ...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. / : / Fervidolysin N-terminal prodomain / Trypsin Inhibitor V; Chain A / Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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
Subtilisin BPN' / Subtilisin-chymotrypsin inhibitor-2A
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
Hordeum sp. (barley)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsMcphalen, C.A. / James, M.N.G.
Citation
Journal: Biochemistry / Year: 1988
Title: Structural comparison of two serine proteinase-protein inhibitor complexes: eglin-c-subtilisin Carlsberg and CI-2-subtilisin Novo.
Authors: McPhalen, C.A. / James, M.N.
#1: Journal: Biochemistry / Year: 1987
Title: Crystal and Molecular Structure of the Serine Proteinase Inhibitor Ci-2 from Barley Seeds
Authors: Mcphalen, C.A. / James, M.N.G.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1985
Title: Crystal and Molecular Structure of Chymotrypsin Inhibitor 2 from Barley Seeds in Complex with Subtilisin Novo
Authors: Mcphalen, C.A. / Svendsen, I. / Jonassen, I. / James, M.N.G.
History
DepositionSep 5, 1988Processing site: BNL
SupersessionSep 7, 1988ID: 1SNI
Revision 1.0Sep 7, 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 21, 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.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
Remark 700SHEET THE CROSS-OVER CONNECTION BETWEEN STRANDS 1 AND 2 OF SHEET S1E IS LEFT-HANDED. THE BETA-SHEET ...SHEET THE CROSS-OVER CONNECTION BETWEEN STRANDS 1 AND 2 OF SHEET S1E IS LEFT-HANDED. THE BETA-SHEET OF THE INHIBITOR IS IRREGULAR , WITH WELL-ORDERED WATER MOLECULES PROVIDING ALL BUT ONE HYDROGEN-BONDING BRIDGE BETWEEN STRANDS 2 AND 3. SEE THE PAPER CITED ON THE *JRNL* RECORDS ABOVE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: SUBTILISIN NOVO
I: CHYMOTRYPSIN INHIBITOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8964
Polymers36,8162
Non-polymers802
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-24 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.190, 56.830, 68.740
Angle α, β, γ (deg.)90.00, 127.47, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: SEE REMARK 7. / 2: RESIDUE CYS E 168 IS A CIS PROLINE.

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Components

#1: Protein SUBTILISIN NOVO


Mass: 27551.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / References: UniProt: P00782, 3.4.21.14
#2: Protein CHYMOTRYPSIN INHIBITOR 2


Mass: 9264.659 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum sp. (barley) / References: UniProt: P01053
#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


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ORDER OF THE FIRST FOUR RESIDUES OF CHAIN *I* IS UNKNOWN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion, hanging drop
Details: McPhalen, C.A., (1985) Proc. Natl. Acad. Sci. USA., 82, 7242.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.4 Mammonium sulfate1reservoir
250 mM1reservoirKH2PO4

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.1→8 Å / σ(I): 1
Details: WATER MOLECULES WITH SEQUENCE NUMBERS 600 - 602 AND B VALUES OF 0.0 WERE ADDED AT THE POSITIONS OF STRONG PEAKS IN THE FINAL DIFFERENCE MAP, AND THEIR POSITIONS HAVE NOT BEEN REFINED.
RfactorNum. reflection
obs0.154 16128
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 2 168 2621
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0060.008
X-RAY DIFFRACTIONp_angle_d0.0240.016
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0180.016
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0130.012
X-RAY DIFFRACTIONp_chiral_restr0.1190.08
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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