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- PDB-1ds3: CRYSTAL STRUCTURE OF OMTKY3-CH2-ASP19I -

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Basic information

Entry
Database: PDB / ID: 1ds3
TitleCRYSTAL STRUCTURE OF OMTKY3-CH2-ASP19I
ComponentsOVOMUCOID
KeywordsHYDROLASE INHIBITOR / canonical protein inhibitor / ovomucoid / reduced peptide bond / OMTKY3
Function / homology
Function and homology information


molecular function inhibitor activity / serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMeleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / Resolution: 1.65 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: Version format compliance
Revision 1.3Aug 17, 2011Group: Non-polymer description
Revision 1.4Nov 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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: OVOMUCOID


Theoretical massNumber of molelcules
Total (without water)5,5571
Polymers5,5571
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.152, 36.092, 26.135
Angle α, β, γ (deg.)90.00, 97.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein OVOMUCOID /


Mass: 5557.278 Da / Num. of mol.: 1 / Fragment: THIRD DOMAIN (OMTKY3) / Mutation: REDUCED PEPTIDE BOND BETWEEN LEU18I(2LU)-ASP19I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey)
Description: THE PEPTIDE BOND BETWEEN LEU18I(2LU) AND ASP19I HAS BEEN REDUCED.
Production host: Escherichia coli (E. coli) / References: UniProt: P68390
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 1.95 Å3/Da / Density % sol: 37.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: ammonium sulphate, no buffer, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
22.0 Mammonium sulfate1reservoir

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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: Apr 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 16933 / % possible obs: 92.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.64
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.245 / % possible all: 47.6
Reflection
*PLUS
Num. obs: 4800 / Num. measured all: 16933
Reflection shell
*PLUS
% possible obs: 47.6 %

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Processing

Software
NameVersionClassification
XPRESSdata collection
SCALEPACKdata scaling
AMoREphasing
TNT5Erefinement
XPRESSdata reduction
RefinementResolution: 1.65→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.23 -Random. 5%
Rwork0.196 --
obs-4800 -
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms385 0 0 41 426
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg1.115
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.011

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