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- PDB-4sgb: STRUCTURE OF THE COMPLEX OF STREPTOMYCES GRISEUS PROTEINASE B AND... -

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Basic information

Entry
Database: PDB / ID: 4sgb
TitleSTRUCTURE OF THE COMPLEX OF STREPTOMYCES GRISEUS PROTEINASE B AND POLYPEPTIDE CHYMOTRYPSIN INHIBITOR-1 FROM RUSSET BURBANK POTATO TUBERS AT 2.1 ANGSTROMS RESOLUTION
Components
  • POTATO INHIBITOR, PCI-1
  • SERINE PROTEINASE B
KeywordsCOMPLEX(SERINE PROTEINASE-INHIBITOR)
Function / homology
Function and homology information


streptogrisin B / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Proteinase inhibitor I20 / : / Potato type II proteinase inhibitor family / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site ...Proteinase inhibitor I20 / : / Potato type II proteinase inhibitor family / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Streptogrisin-B / Proteinase inhibitor type-2 K
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsJames, M. / Greenblatt, H.
CitationJournal: J.Mol.Biol. / Year: 1989
Title: Structure of the complex of Streptomyces griseus proteinase B and polypeptide chymotrypsin inhibitor-1 from Russet Burbank potato tubers at 2.1 A resolution.
Authors: Greenblatt, H.M. / Ryan, C.A. / James, M.N.
History
DepositionSep 21, 1989Processing site: BNL
Revision 1.0Jul 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 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_ref_seq_dif / struct_sheet / 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_PDB_ins_code / _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_PDB_ins_code / _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.pdbx_ptnr2_PDB_ins_code / _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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: SERINE PROTEINASE B
I: POTATO INHIBITOR, PCI-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4075
Polymers24,1752
Non-polymers2323
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-39 kcal/mol
Surface area9790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.920, 46.200, 52.530
Angle α, β, γ (deg.)90.00, 117.08, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES PRO E 95 IS A CIS PROLINE.

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Components

#1: Protein SERINE PROTEINASE B


Mass: 18665.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus (bacteria) / References: UniProt: P00777
#2: Protein POTATO INHIBITOR, PCI-1


Mass: 5509.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P01080
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTWO SULFATE IONS HAVE BEEN IDENTIFIED. THERE ARE 180 SOLVENT POSITIONS. AMONG THESE, THE ONE AT ...TWO SULFATE IONS HAVE BEEN IDENTIFIED. THERE ARE 180 SOLVENT POSITIONS. AMONG THESE, THE ONE AT POSITION 8 IS CONSIDERED AS A POSSIBLE CA2+ ION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal grow
*PLUS
Temperature: 292-296 K / Method: vapor diffusion, hanging drop / PH range low: 7.2 / PH range high: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 %sat1reservoir(NH4)2SO4
20.1 Mpotasssium phosphate1reservoir
33 %(v/v)MPD1reservoir

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Data collection

Reflection
*PLUS
Num. measured all: 12941

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.1→8 Å /
RfactorNum. reflection
obs0.142 12685
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 11 179 1880
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.015
X-RAY DIFFRACTIONp_angle_d0.040.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.03
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_restr0.0140.015
X-RAY DIFFRACTIONp_chiral_restr0.2130.15
X-RAY DIFFRACTIONp_singtor_nbd0.2030.3
X-RAY DIFFRACTIONp_multtor_nbd0.1530.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1430.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.42.5
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 8 Å / Num. reflection obs: 12685 / Rfactor obs: 0.142
Solvent computation
*PLUS
Displacement parameters
*PLUS

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