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- PDB-1ds2: CRYSTAL STRUCTURE OF SGPB:OMTKY3-COO-LEU18I -

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Basic information

Entry
Database: PDB / ID: 1ds2
TitleCRYSTAL STRUCTURE OF SGPB:OMTKY3-COO-LEU18I
Components
  • OVOMUCOID
  • PROTEINASE B (SGPB)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / serine proteinase / protein inhibitor / ovomucoid / canonical inhibitor / ester bond / SGPB / OMTKY3 / HYDROLASE-HYDROLASE 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
Streptogrisin-B / Ovomucoid
Similarity search - Component
Biological speciesMeleagris gallopavo (turkey)
Streptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsBateman, K.S. / Huang, K. / Anderson, S. / Lu, W. / Qasim, M.A. / Laskowski Jr., M. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Contribution of peptide bonds to inhibitor-protease binding: crystal structures of the turkey ovomucoid third domain backbone variants OMTKY3-Pro18I and OMTKY3-psi[COO]-Leu18I in complex with ...Title: Contribution of peptide bonds to inhibitor-protease binding: crystal structures of the turkey ovomucoid third domain backbone variants OMTKY3-Pro18I and OMTKY3-psi[COO]-Leu18I in complex with Streptomyces griseus proteinase B (SGPB) and the structure of the free inhibitor, OMTKY-3-psi[CH2NH2+]-Asp19I
Authors: Bateman, K.S. / Huang, K. / Anderson, S. / Lu, W. / Qasim, M.A. / Laskowski Jr., M. / James, M.N.
History
DepositionJan 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: PROTEINASE B (SGPB)
I: OVOMUCOID


Theoretical massNumber of molelcules
Total (without water)24,2522
Polymers24,2522
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-9 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.413, 54.647, 45.525
Angle α, β, γ (deg.)90.00, 119.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEINASE B (SGPB) / STREPTOGRISIN B


Mass: 18665.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces griseus (bacteria) / References: UniProt: P00777, streptogrisin B
#2: Protein OVOMUCOID


Mass: 5586.273 Da / Num. of mol.: 1 / Fragment: THIRD DOMAIN (OMTKY3) / Mutation: ESTER BOND BETWEEN THR17I-LEU18I(1LU)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey)
Description: THE PEPTIDE LINKAGE BETWEEN THR17I AND LEU18I(1LU) HAS BEEN REPLACED BY AN ESTER BOND.
Production host: Escherichia coli (E. coli) / References: UniProt: P68390
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: PEG 4000, sodium potassium phosphate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Details: used seeding / PH range low: 7.1 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mM1reservoirpH6.5-7..1NaKH-PO4
2PEG40001reservoir
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 61078 / % possible obs: 87.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.86
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.288 / % possible all: 47.1
Reflection
*PLUS
Num. obs: 18894 / Num. measured all: 61078 / Rmerge(I) obs: 0.12
Reflection shell
*PLUS
Highest resolution: 1.71 Å / % possible obs: 47.1 %

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Processing

Software
NameVersionClassification
XPRESSdata collection
SCALEPACKdata scaling
X-PLORmodel building
TNT5Erefinement
XPRESSdata reduction
X-PLORphasing
RefinementResolution: 1.7→20 Å / Stereochemistry target values: Engh & Huber /
RfactorNum. reflection
obs0.183 18894
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 0 140 1837
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg0.985
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor all: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.012

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