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- PDB-1sib: REFINED CRYSTAL STRUCTURES OF SUBTILISIN NOVO IN COMPLEX WITH WIL... -

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Basic information

Entry
Database: PDB / ID: 1sib
TitleREFINED CRYSTAL STRUCTURES OF SUBTILISIN NOVO IN COMPLEX WITH WILD-TYPE AND TWO MUTANT EGLINS. COMPARISON WITH OTHER SERINE PROTEINASE INHIBITOR COMPLEXES
Components
  • EGLIN C
  • SUBTILISIN NOVO BPN'
KeywordsSERINE PROTEASE/INHIBITOR COMPLEX / SERINE PROTEASE-INHIBITOR COMPLEX / SERINE PROTEASE-INHIBITOR COMPLEX 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' / Eglin C
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsGruetter, M.G. / Heinz, D.W. / Priestle, J.P.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Refined crystal structures of subtilisin novo in complex with wild-type and two mutant eglins. Comparison with other serine proteinase inhibitor complexes.
Authors: Heinz, D.W. / Priestle, J.P. / Rahuel, J. / Wilson, K.S. / Grutter, M.G.
#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
DepositionAug 2, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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 14, 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_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_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

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Assembly

Deposited unit
E: SUBTILISIN NOVO BPN'
I: EGLIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7054
Polymers35,6252
Non-polymers802
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-20 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.900, 84.900, 89.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: RESIDUE PRO E 168 IS A CIS PROLINE.

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Components

#1: Protein SUBTILISIN NOVO BPN'


Mass: 27552.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / References: UniProt: P00782, subtilisin
#2: Protein EGLIN C


Mass: 8071.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Production host: Escherichia coli (E. coli) / 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


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160 mg/mlprotein1drop
210-15 %(w/v)PEG40001reservoir
30.1 Mpotassium phosphate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 24538 / Rmerge(I) obs: 0.097 / Num. measured all: 74306

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.4→5 Å / σ(F): 0 /
RfactorNum. reflection
obs0.159 11195
Refinement stepCycle: LAST / Resolution: 2.4→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 2 195 2655
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0480.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it4.194
X-RAY DIFFRACTIONp_mcangle_it6.236
X-RAY DIFFRACTIONp_scbond_it12.710
X-RAY DIFFRACTIONp_scangle_it15.215
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1510.15
X-RAY DIFFRACTIONp_singtor_nbd0.220.5
X-RAY DIFFRACTIONp_multtor_nbd0.30.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.30.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.93
X-RAY DIFFRACTIONp_staggered_tor21.815
X-RAY DIFFRACTIONp_orthonormal_tor3920
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 5 Å / Num. reflection obs: 11195 / σ(F): 0 / Rfactor obs: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS

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