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- PDB-2aiz: Solution structure of peptidoglycan associated lipoprotein from H... -

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Basic information

Entry
Database: PDB / ID: 2aiz
TitleSolution structure of peptidoglycan associated lipoprotein from Haemophilus influenza bound to UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine
Components
  • L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine
  • Outer membrane protein P6 (Fragment)
KeywordsMEMBRANE PROTEIN / alpha-beta sandwich / Structure 2 Function Project / S2F / Structural Genomics
Function / homology
Function and homology information


cell cycle / cell outer membrane / membrane => GO:0016020 / cell division
Similarity search - Function
Peptidoglycan-associated lipoprotein, C-terminal / Peptidoglycan-associated lipoprotein / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. ...Peptidoglycan-associated lipoprotein, C-terminal / Peptidoglycan-associated lipoprotein / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / 60s Ribosomal Protein L30; Chain: A; / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-beta-muramic acid / URIDINE-5'-DIPHOSPHATE / Outer membrane protein P6 / Peptidoglycan-associated lipoprotein
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
synthetic construct (others)
MethodSOLUTION NMR
AuthorsParsons, L.M. / Lin, F. / Orban, J. / Structure 2 Function Project (S2F)
CitationJournal: Biochemistry / Year: 2006
Title: Peptidoglycan recognition by pal, an outer membrane lipoprotein.
Authors: Parsons, L.M. / Lin, F. / Orban, J.
History
DepositionAug 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Feb 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / diffrn / diffrn_radiation / diffrn_radiation_wavelength / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_oper_list / struct_asym / struct_conn / struct_ref / struct_ref_seq
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.label_seq_id / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Outer membrane protein P6 (Fragment)
U: L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4824
Polymers14,7842
Non-polymers6972
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Outer membrane protein P6 (Fragment)


Mass: 14250.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: ompP6 / Plasmid: pet28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: M4PH67, UniProt: P10324*PLUS
#2: Protein/peptide L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine


Mass: 533.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Sugar ChemComp-AMU / N-acetyl-beta-muramic acid / N-acetyl-muramic acid / BETA-N-ACETYLMURAMIC ACID


Type: D-saccharide, beta linking / Mass: 293.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO8
IdentifierTypeProgram
b-D-GlcpNAc3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
MurNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1323D 13C-separated NOESY
1422D NOESY
1533D 13C-separated NOESY
1622D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM PAL + UYP; 15N/13C. 50mM phosphate 50mM NaCL, pH6.7, 90% H2O, 10% D2O90% H2O/10% D2O
20.8mM PAL + UYP; 15N/13C. 50mM phosphate 50mM NaCL, pH6.7, 100% D2OD2O
30.8mM PAL(unlabeled) + UYP(15N/13C). 50mM phosphate 50mM NaCL, pH6.7, 100% D2OD2O
40.8mM PAL + UYP; 15N/13C. 50mM phosphate 50mM NaCL, pH6.7, phage, 90% H2O 10% D2O90% H2O/10% D2O
51mM UYP 15N/13C, 100% D2OD2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM phosphate, 50mM NaCl 6.7ambient 298 K
250mM phosphate, 50mM NaCl 6.7ambient 298 K
350mM phosphate, 50mM NaCl 6.7ambient 298 K
450mM phosphate, 50mM NaCl 6.7ambient 298 K
550mM phosphate, 50mM NaCl 6.7ambient 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1A.T.Brunger,P.D.Adams,G.M.Clore,W.L.Delano,P.Gros,R.W.Grosse-Kunstleve,J.-S.Jiang,J.Kuszewski,M.Nilges,N.S.Pannu,R.J.Read,L.M.Rice,T.Simonson,G.L.Warrenrefinement
Sparky2.4T.D.Goddard,D.G.Knellerdata analysis
NMRPipe1F.Delaglio,S.Grzesiek,G.W.Vuister,G.Zhu,J.Pfeifer,A.Baxprocessing
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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