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- PDB-1sgr: LEU 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1sgr
TitleLEU 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B
Components
  • STREPTOMYCES GRISEUS PROTEINASE B
  • TURKEY OVOMUCOID INHIBITOR
KeywordsCOMPLEX (SERINE PROTEASE/INHIBITOR) / SERINE PROTEINASE / PROTEIN INHIBITOR / COMPLEX (SERINE PROTEASE-INHIBITOR) COMPLEX
Function / homology
Function and homology information


streptogrisin B / molecular function inhibitor activity / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain ...Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / 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
PHOSPHATE ION / Streptogrisin-B / Ovomucoid
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
Meleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsHuang, K. / James, M.N.G.
Citation
Journal: Protein Sci. / Year: 1995
Title: Water molecules participate in proteinase-inhibitor interactions: crystal structures of Leu18, Ala18, and Gly18 variants of turkey ovomucoid inhibitor third domain complexed with Streptomyces griseus proteinase B.
Authors: Huang, K. / Lu, W. / Anderson, S. / Laskowski Jr., M. / James, M.N.
#1: Journal: Biochemistry / Year: 1983
Title: Structure of the Complex of Streptomyces Griseus Protease B and the Third Domain of the Turkey Ovomucoid Inhibitor at 1.8 Angstroms Resolution
Authors: Read, R.J. / Fujinaga, M. / Sielecki, A.R. / James, M.N.G.
History
DepositionMay 26, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: 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 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _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: STREPTOMYCES GRISEUS PROTEINASE B
I: TURKEY OVOMUCOID INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3463
Polymers24,2512
Non-polymers951
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-15 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.530, 54.660, 45.590
Angle α, β, γ (deg.)90.00, 119.19, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO E 99A / 2: CIS PROLINE - PRO I 12

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Components

#1: Protein STREPTOMYCES GRISEUS PROTEINASE B


Mass: 18665.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus (bacteria) / Strain: K1 / Plasmid: PEZZ318.TKY / Production host: Escherichia coli (E. coli) / References: UniProt: P00777, streptogrisin B
#2: Protein TURKEY OVOMUCOID INHIBITOR / LEU18-OMTKY3


Mass: 5585.289 Da / Num. of mol.: 1 / Mutation: DEL(1-6)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey) / Plasmid: PEZZ318.TKY / Production host: Escherichia coli (E. coli) / References: UniProt: P68390
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 39.75 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
22 %PEG60001drop
350 mMsodium potassium phosphate1drop
42 %PEG60001reservoir
550 mMsodium potassium phosphate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE MARK II / Detector: AREA DETECTOR / Date: Jan 10, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 2.4 % / Rmerge(I) obs: 0.053
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 17183 / % possible obs: 94.3 % / Num. measured all: 41124 / Rmerge(I) obs: 0.0529
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 2 Å / % possible obs: 51.1 %

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Processing

Software
NameClassification
BIOMOLdata collection
TNTrefinement
BIOMOLdata reduction
RefinementResolution: 1.8→20 Å / σ(F): 1 /
RfactorNum. reflection
obs0.136 17165
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 5 169 1871
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.02
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Rfactor obs: 0.139
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.022
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.4
X-RAY DIFFRACTIONt_plane_restr0.022

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