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- PDB-1ct0: CRYSTAL STRUCTURE OF THE OMTKY3 P1 VARIANT OMTKY3-SER18I IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 1ct0
TitleCRYSTAL STRUCTURE OF THE OMTKY3 P1 VARIANT OMTKY3-SER18I IN COMPLEX WITH SGPB
Components
  • OVOMUCOID INHIBITOR
  • PROTEINASE B
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ENZYME-INHIBITOR COMPLEX / BETA-BRANCHED P1 RESIDUE / 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 ...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: 1.8 Å
AuthorsBateman, K.S. / Anderson, S. / Lu, W. / Qasim, M.A. / Laskowski Jr., M. / James, M.N.G.
CitationJournal: Protein Sci. / Year: 2000
Title: Deleterious effects of beta-branched residues in the S1 specificity pocket of Streptomyces griseus proteinase B (SGPB): crystal structures of the turkey ovomucoid third domain variants Ile18I, ...Title: Deleterious effects of beta-branched residues in the S1 specificity pocket of Streptomyces griseus proteinase B (SGPB): crystal structures of the turkey ovomucoid third domain variants Ile18I, Val18I, Thr18I, and Ser18I in complex with SGPB.
Authors: Bateman, K.S. / Anderson, S. / Lu, W. / Qasim, M.A. / Laskowski Jr., M. / James, M.N.
History
DepositionAug 18, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: PROTEINASE B
I: OVOMUCOID INHIBITOR


Theoretical massNumber of molelcules
Total (without water)24,2242
Polymers24,2242
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-7 kcal/mol
Surface area9710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.522, 54.590, 45.582
Angle α, β, γ (deg.)90.00, 119.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEINASE B / SGPB


Mass: 18665.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces griseus (bacteria) / Strain: K1 / References: UniProt: P00777, streptogrisin B
#2: Protein OVOMUCOID INHIBITOR


Mass: 5559.208 Da / Num. of mol.: 1 / Fragment: THIRD DOMAIN SER18-OMTKY3 / Mutation: DEL 1-5, L18S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey) / Cell: EGG / Plasmid: PEZZ318.TKY / Production host: Escherichia coli (E. coli) / References: UniProt: P68390
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 4000 sodium potassium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19 mg/mlprotein1drop
24-10 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAC Science DIP-2000H / Detector: IMAGE PLATE / Date: Sep 2, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 112593 / % possible obs: 96.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 7.71
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.455 / % possible all: 72
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 15363 / % possible obs: 99.2 % / Num. measured all: 57863 / Rmerge(I) obs: 0.118
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.93 Å / % possible obs: 99.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.16

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Processing

Software
NameVersionClassification
DIPXPRESSdata collection
SCALEPACKdata scaling
X-PLORmodel building
TNTrefinement
DIPXPRESSdata reduction
X-PLORphasing
RefinementResolution: 1.8→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
all0.169 18888 -
obs--96.7 %
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1703 0 0 152 1855
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg1.051
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Num. reflection all: 15363 / Rfactor all: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.013

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