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- PDB-2gi9: Backbone Conformational Constraints in a Microcrystalline U-15N-L... -

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Basic information

Entry
Database: PDB / ID: 2gi9
TitleBackbone Conformational Constraints in a Microcrystalline U-15N-Labeled Protein by 3D Dipolar-Shift Solid-State NMR Spectroscopy
ComponentsImmunoglobulin B1 binding domain of protein G
KeywordsIMMUNE SYSTEM / Protein binding / GB1
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 speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.14 Å
AuthorsFranks, W.T. / Wylie, B.J. / Stellfox, S.A. / Rienstra, C.M.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Backbone Conformational Constraints in a Microcrystalline U-15N-Labeled Protein by 3D Dipolar-Shift Solid-State NMR Spectroscopy
Authors: Franks, W.T. / Wylie, B.J. / Stellfox, S.A. / Rienstra, C.M.
History
DepositionMar 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 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 B1 binding domain of protein G


Theoretical massNumber of molelcules
Total (without water)6,2291
Polymers6,2291
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.197, 36.384, 50.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein Immunoglobulin B1 binding domain of protein G / IgG binding protein G


Mass: 6228.809 Da / Num. of mol.: 1 / Mutation: T2Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: spg / Production host: Escherichia coli (E. coli) / References: UniProt: P19909
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 36 %
Crystal growpH: 4.5
Details: 5mM Acetate 3.8, 150mM NaCl, 50% MPD and 20% IPA, pH 4.5

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.14→50 Å / Num. obs: 16662 / % possible obs: 96.3 % / Observed criterion σ(I): 0

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.14→50 Å / Num. parameters: 3 / Num. restraintsaints: 1803 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.181 787 0 %RANDOM
all0.193 16502 --
obs0.167 -94.6 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 557
Refinement stepCycle: LAST / Resolution: 1.14→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms438 0 0 119 557
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0.063
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.084
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.075
X-RAY DIFFRACTIONs_approx_iso_adps0
NMR ensembleConformers submitted total number: 1

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