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- PDB-1q2n: REFINED Solution NMR structure of the Z domain of STAPHYLOCOCCAL ... -

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Basic information

Entry
Database: PDB / ID: 1q2n
TitleREFINED Solution NMR structure of the Z domain of STAPHYLOCOCCAL PROTEIN A
ComponentsIMMUNOGLOBULIN G BINDING PROTEIN A
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN-BINDING PROTEIN / THREE-HELICAL BUNDLE STRUCTURE / RESIDUAL DIPOLAR COUPLINGS
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Immunoglobulin FC, subunit C / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Octapeptide repeat / Octapeptide repeat / Immunoglobulin FC, subunit C / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / SIMULATED ANNEALING WITH RESTRAINED MOLECULAR DYNAMICS, PROTOCAL USED: ANNEAL.INP
AuthorsZheng, D. / Tashiro, M. / Aramini, J.M. / Montelione, G.T.
Citation
Journal: Protein Sci. / Year: 2004
Title: Validation of helical tilt angles in the solution NMR structure of the Z domain of Staphylococcal protein A by combined analysis of residual dipolar coupling and NOE data.
Authors: Zheng, D. / Aramini, J.M. / Montelione, G.T.
#1: Journal: Biochemistry / Year: 1996
Title: The Mechanism of Binding Staphylococcal Protein a to Immunoglobin G Does not Involve Helix Unwinding
Authors: Jendeberg, L. / Tashiro, M. / Tejero, R. / Lyons, B.A. / Uhlen, M. / Montelione, G.T. / Nilsson, B.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 1995
Title: Structures of Bacterial Immunoglobulin-Binding Domains and Their Complexes with Immunoglobulin
Authors: Tashiro, M. / Montelione, G.T.
#3: Journal: Biochemistry / Year: 1993
Title: An Improved Strategy for Determining Resonance Assignments for Isotopically Enriched Proteins and its Application to an Engineered Domain of Staphylococcal Protein A
Authors: Lyons, B.A. / Tashiro, M. / Cedergren, L. / Nilsson, B. / Montelione, G.T.
#4: Journal: J.Mol.Biol. / Year: 1997
Title: High Resolution Solution NMR Structure of the Z Domain of Staphylococcal Protein A
Authors: Tashiro, M. / Tejero, R. / Zimmerman, D.E. / Celda, B. / Nilsson, B. / Montelione, G.T.
History
DepositionJul 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / 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

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Assembly

Deposited unit
A: IMMUNOGLOBULIN G BINDING PROTEIN A


Theoretical massNumber of molelcules
Total (without water)6,6481
Polymers6,6481
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Antibody IMMUNOGLOBULIN G BINDING PROTEIN A / IGG binding protein A


Mass: 6648.316 Da / Num. of mol.: 1 / Fragment: residues 212-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Cellular location: CELL WALL / Plasmid: PDHZ / Production host: Escherichia coli (E. coli) / Strain (production host): RV308 / References: UniProt: P38507

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: NMR EXPERIMENTS CONDUCTED: 2D PFG-[15N]HSQC, 3D PFG-HNCO, 3D PFG-(HA)CA(CO)NH, 3D PFG-HA(CA)(CO)NH, 3D PFG-HA(CA)NH, 3D PFG-CBCANH, 3D PFG-CBCA(CO)NH, 3D PFG- (HA)CANH, 3D PFG-HN(CA)CO, 3D PFG- ...Text: NMR EXPERIMENTS CONDUCTED: 2D PFG-[15N]HSQC, 3D PFG-HNCO, 3D PFG-(HA)CA(CO)NH, 3D PFG-HA(CA)(CO)NH, 3D PFG-HA(CA)NH, 3D PFG-CBCANH, 3D PFG-CBCA(CO)NH, 3D PFG- (HA)CANH, 3D PFG-HN(CA)CO, 3D PFG-HCCNH-TOCSY, 3D PFG-HCC (CO)NH-TOCSY, 2D [15N]HSQC-IPAP, 3D Ca-coupled HNCO

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Sample preparation

DetailsContents: 1mM Z domain U-15N,13C; 20mM NH4OAc buffer; 95% H2O, 5% D2O.
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 20 mM NH4OAc / pH: 6.50 / Pressure: 1 atm / Temperature: 303.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian MODIFIED UNITY 500 / Manufacturer: Varian / Model: MODIFIED UNITY 500 / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1BRUNGER, A.T.refinement
CNS1BRUNGER, A.T.structure solution
RefinementMethod: SIMULATED ANNEALING WITH RESTRAINED MOLECULAR DYNAMICS, PROTOCAL USED: ANNEAL.INP
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 769 CONFORMATIONAL RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE CONSTRAINTS: TOTAL = 536; INTRA-RESIDUE [I=J] = 224; SEQUENTIAL [(I-J)=1] ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 769 CONFORMATIONAL RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE CONSTRAINTS: TOTAL = 536; INTRA-RESIDUE [I=J] = 224; SEQUENTIAL [(I-J)=1] = 142; MEDIUM RANGE [1<(I-J)<5] 105; LONG RANGE [(I-J)>=5] = 65; NUMBER OF DISTANCE CONSTRAINTS RESIDUE = 9.2; DIHEDRAL-ANGLE CONSTRAINTS = 107 RESIDUAL DIPOLAR COUPLING CONSTRAINTS = 126 (34 N-H, 43 HA-CA, 4 TOTAL NUMBER OF CONSTRAINTS PER RESIDUE = 13.3; NUMBER OF LONG RANGE CONSTRAINTS PER RESIDUE = 3.3; NUMBER OF STRUCTURES COMPUTED = 100; NUMBER OF STRUCTURES USED = 10. AVERAGE RESIDUAL CONSTRAINT VIOLATIONS: DISTANCE VIOLATIONS 0.1-0.2 ANG = 7.7, 0. 0.8, >0.5 ANG = 0.3. AVERAGE R.M.S. DISTANCE VIOLATION = 0.03 AN AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0 DEG = 0; RMSD VALUES: BACKBONE ATOMS (N,C,C') = 1.2 ANG; BACKBONE ATOMS(N,C,C') OF ORDERED RESIDUES = 0.4 ANG; ALL HEAVY = 1.7 ANG; ALL HEAVY ATOMS OF ORDERED RESIDUES = 1.0 ANG. PROCHECK USING ORDERED RESIDUES (5-36,39-57): MOST FAVORED REGIONS = 91.4%; ADDITIONAL ALLOWED REGIONS = 8.4%; GENEROUSLY ALLOWED REGIONS = 0.2%; DISALLOWED REGIONS = 0%.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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