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- PDB-3v3x: Nitroxide Spin Labels in Protein GB1: N8/K28 Double Mutant -

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Basic information

Entry
Database: PDB / ID: 3v3x
TitleNitroxide Spin Labels in Protein GB1: N8/K28 Double Mutant
ComponentsImmunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / domain-swapped dimer / nitroxide spin label
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / 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 / M protein-type anchor domain / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / 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
ACETATE ION / Chem-MTN / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. 'group G' (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCunningham, T.F. / McGoff, M.S. / Sengupta, I. / Jaroniec, C.P. / Horne, W.S. / Saxena, S.K.
CitationJournal: Biochemistry / Year: 2012
Title: High-resolution structure of a protein spin-label in a solvent-exposed beta-sheet and comparison with DEER spectroscopy.
Authors: Cunningham, T.F. / McGoff, M.S. / Sengupta, I. / Jaroniec, C.P. / Horne, W.S. / Saxena, S.
History
DepositionDec 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G
B: Immunoglobulin G-binding protein G
C: Immunoglobulin G-binding protein G
D: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,24315
Polymers24,7674
Non-polymers2,47511
Water2,324129
1
A: Immunoglobulin G-binding protein G
C: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5916
Polymers12,3842
Non-polymers1,2084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-28 kcal/mol
Surface area6830 Å2
MethodPISA
2
B: Immunoglobulin G-binding protein G
D: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6519
Polymers12,3842
Non-polymers1,2687
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-30 kcal/mol
Surface area7330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.248, 35.747, 86.989
Angle α, β, γ (deg.)90.00, 126.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 1 types, 4 molecules ABCD

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


Mass: 6191.812 Da / Num. of mol.: 4 / Mutation: C8N
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: P19909

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Non-polymers , 5 types, 140 molecules

#2: Chemical
ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL / MTSL


Mass: 264.385 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H18NO3S2
#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 150 mM sodium acetate pH 4.5, 18% w/v PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 19, 2011 / Details: Rigaku VariMax Optics
RadiationMonochromator: Rigaku VariMax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→27.3 Å / Num. obs: 17743 / % possible obs: 98.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.5

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.6.0117refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2QMT

2qmt


Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.876 / SU B: 5.218 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28793 907 5.1 %RANDOM
Rwork0.22818 ---
obs0.2313 16835 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.042 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å2-0.2 Å2
2---0.02 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1724 0 93 129 1946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021914
X-RAY DIFFRACTIONr_bond_other_d0.0090.021144
X-RAY DIFFRACTIONr_angle_refined_deg2.1652.0122635
X-RAY DIFFRACTIONr_angle_other_deg1.7053.0062826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1095232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57227.10883
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49415302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022097
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02347
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 70 -
Rwork0.281 1110 -
obs--94.55 %

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