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- PDB-2nu4: Accommodation of positively-charged residues in a hydrophobic spe... -

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Basic information

Entry
Database: PDB / ID: 2nu4
TitleAccommodation of positively-charged residues in a hydrophobic specificity pocket: Crystal structures of SGPB in complex with OMTKY3 variants Lys18I and Arg18I
Components
  • Ovomucoid
  • Streptogrisin B, Proteinase B
KeywordsHYDROLASE / ENZYME-INHIBITOR COMPLEX / CHARGED P1 RESIDUE
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 / MIR / Resolution: 1.75 Å
AuthorsBateman, K.S. / Anderson, S. / Lu, W. / Qasim, M.A. / Laskowski Jr., M. / James, M.N.G.
CitationJournal: To be Published
Title: Accommodation of positively-charged residues in a hydrophobic specificity pocket: Crystal structures of SGPB in complex with OMTKY3 variants Lys18I and Arg18I
Authors: Bateman, K.S. / Anderson, S. / Lu, W. / Qasim, M.A. / Laskowski Jr., M. / James, M.N.G.
History
DepositionNov 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Streptogrisin B, Proteinase B
I: Ovomucoid


Theoretical massNumber of molelcules
Total (without water)24,2552
Polymers24,2552
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.452, 54.689, 45.633
Angle α, β, γ (deg.)90.00, 119.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Streptogrisin B, Proteinase B / Protease B / SGPB / Pronase enzyme B


Mass: 18653.232 Da / Num. of mol.: 1 / Fragment: residues 115-299 / Source method: isolated from a natural source / Source: (natural) Streptomyces griseus (bacteria) / Strain: K1 / References: UniProt: P00777, streptogrisin B
#2: Protein Ovomucoid


Mass: 5601.311 Da / Num. of mol.: 1 / Fragment: third domain, residues 135-185 / Mutation: L18K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meleagris gallopavo (turkey) / Plasmid: PEZZ318 / Production host: Escherichia coli (E. coli) / References: UniProt: P68390
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 39.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG 4000, SODIUM POTASSIUM PHOSPHATE at pH 7.1 24h before data collection, crystal was transferred to PEG4000, NaKHPO4 at pH 10.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Mar 28, 1998 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 19840 / Num. obs: 19056 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 3.6 % / Rmerge(I) obs: 0.173 / Net I/σ(I): 8.59
Reflection shellResolution: 1.75→1.76 Å / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 1.72 / % possible all: 70.4

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Processing

Software
NameVersionClassification
DIPXPRESSdata collection
X-PLORmodel building
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 3SGB

3sgb


Resolution: 1.75→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.17 --
obs0.17 19056 95.9 %
Refine analyzeLuzzati coordinate error obs: 0.17 Å / Luzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 0 174 1891
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg1.016
X-RAY DIFFRACTIONt_dihedral_angle_d16.273

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