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- PDB-6oh1: IgA1 Protease G5 domain structure -

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Basic information

Entry
Database: PDB / ID: 6oh1
TitleIgA1 Protease G5 domain structure
ComponentsImmunoglobulin A1 protease
KeywordsHYDROLASE / IgA1 / Protease / G5 domain
Function / homology
Function and homology information


IgA-specific metalloendopeptidase / cell wall / : / metalloendopeptidase activity / membrane => GO:0016020 / zinc ion binding / extracellular region
Similarity search - Function
Peptidase M26, N-terminal domain / GLUG / Peptidase M26, C-terminal domain / M26 IgA1-specific Metallo-endopeptidase N-terminal region / M26 IgA1-specific Metallo-endopeptidase C-terminal region / The GLUG motif / : / G5 domain / G5 domain / G5 domain profile. ...Peptidase M26, N-terminal domain / GLUG / Peptidase M26, C-terminal domain / M26 IgA1-specific Metallo-endopeptidase N-terminal region / M26 IgA1-specific Metallo-endopeptidase C-terminal region / The GLUG motif / : / G5 domain / G5 domain / G5 domain profile. / G5 / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Immunoglobulin A1 protease
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodSOLUTION NMR / distance geometry
AuthorsEisenmesser, E.Z. / Chi, Y.C. / Paukovich, N. / Redzic, J.S. / Rahkola, J.T. / Janoff, E.N.
CitationJournal: Protein Sci. / Year: 2019
Title: Streptococcus pneumoniae G5 domains bind different ligands.
Authors: Paukovich, N. / Redzic, J.S. / Chi, Y.C. / Rahkola, J.T. / Issaian, A. / Blue, A. / Hansen, K.C. / Janoff, E.N. / Eisenmesser, E.Z.
History
DepositionApr 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin A1 protease


Theoretical massNumber of molelcules
Total (without water)9,5401
Polymers9,5401
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 8structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein Immunoglobulin A1 protease / IgA1 protease / IgA-specific zinc metalloproteinase


Mass: 9539.762 Da / Num. of mol.: 1 / Fragment: G5 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: iga / Production host: Escherichia coli (E. coli)
References: UniProt: Q54875, IgA-specific metalloendopeptidase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic23D HN(CA)CB
131isotropic23D C(CO)NH

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Sample preparation

DetailsType: solution / Contents: 0.42 mM U-13C,15N, 2H IgA1P G5 domain, 100% D2O / Label: 15N, 13C, 2H sample / Solvent system: 100% D2O
SampleConc.: 0.42 mM / Component: IgA1P G5 domain / Isotopic labeling: U-13C,15N, 2H
Sample conditionsIonic strength: 150 mM / Label: Condition 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Direct DriveVarianDirect Drive9001
Bruker AVANCEBrukerAVANCE8002

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.25data extraction
RefinementCross valid method: THROUGHOUT
Displacement parametersBiso max: 0 Å2 / Biso mean: 0 Å2 / Biso min: 0 Å2
NMR software
NameDeveloperClassification
AnalysisCCPNrefinement
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
AnalysisCCPNchemical shift assignment
AnalysisCCPNpeak picking
RefinementMethod: distance geometry / Software ordinal: 2
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 8 / Conformers submitted total number: 8

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