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- PDB-2k0p: Determination of a Protein Structure in the Solid State from NMR ... -

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Basic information

Entry
Database: PDB / ID: 2k0p
TitleDetermination of a Protein Structure in the Solid State from NMR Chemical Shifts
ComponentsImmunoglobulin G-binding protein G
KeywordsPROTEIN BINDING / solid-state / chemical shift restraints / GB1 / Cell wall / IgG-binding protein / Peptidoglycan-anchor / Secreted
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
MethodSOLID-STATE NMR / MD, MC hybrid refinment against Target Fuction weighted by chemical shift accuracy, a molecular mechanics force field
AuthorsRobustelli, P. / Cavalli, A. / Salvatella, X. / Vendruscolo, M.
Citation
Journal: Structure / Year: 2008
Title: Determination of protein structures in the solid state from NMR chemical shifts.
Authors: Robustelli, P. / Cavalli, A. / Vendruscolo, M.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2007
Title: Solid-state protein-structure determination with proton-detected triple-resonance 3D magic-angle-spinning NMR spectroscopy.
Authors: Zhou, D.H. / Shea, J.J. / Nieuwkoop, A.J. / Franks, W.T. / Wylie, B.J. / Mullen, C. / Sandoz, D. / Rienstra, C.M.
#2: Journal: J.Am.Chem.Soc. / Year: 2007
Title: Proton-detected solid-state NMR spectroscopy of fully protonated proteins at 40 kHz magic-angle spinning.
Authors: Zhou, D.H. / Shah, G. / Cormos, M. / Mullen, C. / Sandoz, D. / Rienstra, C.M.
#3: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Protein structure determination from NMR chemical shifts.
Authors: Cavalli, A. / Salvatella, X. / Dobson, C.M. / Vendruscolo, M.
History
DepositionFeb 11, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,2291
Polymers6,2291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1500target function
RepresentativeModel #1lowest energy

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Components

#1: Antibody Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 6228.809 Da / Num. of mol.: 1 / Fragment: GB1 / Mutation: T2Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. group G (bacteria) / Gene: spg / Production host: Escherichia coli (E. coli) / References: UniProt: P06654

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
Method details: Solid-state structure of Beta-1 Immunoglobulin binding domain of protein G (GB1) solved from Ha, Ca, Cb, and N backbone chemical shifts.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D CC DARR mixing
1212D N(CA)CX
1312D N(CO)CX
1413D NCACX
1513D NCOCX
1613D CAN(COCX)
1712D CC SPC5 DQ mixing
NMR detailsText: For Experimental Data See BMRB Entry 15156

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Sample preparation

DetailsContents: 10 mg/mL [U-100% 13C; U-100% 15N] GB1, 0.5 v/v Methyl Pentane diol, 0.25 v/v Isopropanol
Solvent system: 0.5 v/v Methyl Pentane diol/0.25 v/v Isopropanol
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mg/mLGB1[U-100% 13C; U-100% 15N]1
0.5 v/vMethyl Pentane diol1
0.25 v/vIsopropanol1
Sample conditionsPressure: 1 atm / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Infinity PlusVarianInfinity Plus5001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
ALMOST1.0.0Cavalli, A. et al.structure solution
ALMOST1.0.0Cavalli, A. et al.refinement
RefinementMethod: MD, MC hybrid refinment against Target Fuction weighted by chemical shift accuracy, a molecular mechanics force field
Software ordinal: 1
Details: Structure Selection and Refinement were performed according to CHESHIRE protocol for calculation of structures from NMR Chemical Shifts (Cavalli et al., 2007, PNAS, 104, 9615-9620)
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 1500 / Conformers submitted total number: 1

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