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- PDB-2l97: Solution structure of HtrA PDZ domain from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 2l97
TitleSolution structure of HtrA PDZ domain from Streptococcus pneumoniae
ComponentsPutative serine protease
KeywordsPROTEIN BINDING / HtrA-PDZ
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis
Similarity search - Function
: / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll ...: / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Mainly Beta
Similarity search - Domain/homology
Serine protease / PDZ domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model 1
AuthorsFan, K. / Zhang, J. / Zhang, X. / Tu, X.
Citation
Journal: J.Struct.Biol. / Year: 2011
Title: Solution structure of HtrA PDZ domain from Streptococcus pneumoniae and its interaction with YYF-COOH containing peptides.
Authors: Fan, K. / Zhang, J. / Zhang, X. / Tu, X.
#1: Journal: Biomol.Nmr Assign. / Year: 2010
Title: 1H, 13C and 15N resonance assignment of the PDZ domain of HtrA from Streptococcus pneumoniae
Authors: Fan, K. / Zhang, J. / Shang, Q. / Tu, X.
History
DepositionFeb 2, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative serine protease


Theoretical massNumber of molelcules
Total (without water)14,8911
Polymers14,8911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative serine protease / HtrA


Mass: 14890.758 Da / Num. of mol.: 1 / Fragment: PDZ domain, UNP residues 266-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O06670, UniProt: A0A0H2US63*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D C(CO)NH
1613D HBHA(CO)NH
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D (H)CCH-COSY

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Sample preparation

DetailsContents: 0.6mM [U-99% 13C; U-99% 15N] HtrA-PDZ; 100mM sodium chloride; 25mM sodium phosphate; 2mM DTT; 1.5mM EDTA; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMHtrA-PDZ-1[U-99% 13C; U-99% 15N]1
100 mMsodium chloride-21
25 mMsodium phosphate-31
2 mMDTT-41
1.5 mMEDTA-51
10 %D2O-61
Sample conditionsIonic strength: 0.1 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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