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- PDB-5bmg: Nitroxide Spin Labels in Protein GB1: E15 Mutant -

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Basic information

Entry
Database: PDB / ID: 5bmg
TitleNitroxide Spin Labels in Protein GB1: E15 Mutant
ComponentsImmunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / Bacterial Proteins / Crystallization / Electron Spin Resonance Spectroscopy
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
Chem-MTN / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCunningham, T.C. / Horne, W.S. / Saxena, S.
CitationJournal: Protein Sci. / Year: 2016
Title: Rotameric preferences of a protein spin label at edge-strand beta-sheet sites.
Authors: Cunningham, T.F. / Pornsuwan, S. / Horne, W.S. / Saxena, S.
History
DepositionMay 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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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
E: Immunoglobulin G-binding protein G
F: Immunoglobulin G-binding protein G
G: Immunoglobulin G-binding protein G
H: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,71817
Polymers49,6238
Non-polymers2,0959
Water2,900161
1
A: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4672
Polymers6,2031
Non-polymers2641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8544
Polymers6,2031
Non-polymers6513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,2031
Polymers6,2031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4672
Polymers6,2031
Non-polymers2641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4672
Polymers6,2031
Non-polymers2641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5893
Polymers6,2031
Non-polymers3872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4672
Polymers6,2031
Non-polymers2641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,2031
Polymers6,2031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.323, 79.498, 52.406
Angle α, β, γ (deg.)90.00, 90.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 6202.838 Da / Num. of mol.: 8 / Fragment: UNP residues 304-357 / Mutation: E15C
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
#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: isolated from a genetically manipulated source
Formula: C10H18NO3S2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M magnesium chloride, 0.1 M Tris pH 4.5, 20% w/v PEG 4000

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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: Feb 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→27.11 Å / Num. obs: 21244 / % possible obs: 97.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.7 / % possible all: 90.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QMT

2qmt


Resolution: 2.2→27.075 Å / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 35.09 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2183 1111 5.23 %
Rwork0.1859 --
obs0.1885 21243 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→27.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 16 161 3741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073633
X-RAY DIFFRACTIONf_angle_d1.3154956
X-RAY DIFFRACTIONf_dihedral_angle_d16.7761297
X-RAY DIFFRACTIONf_chiral_restr0.073574
X-RAY DIFFRACTIONf_plane_restr0.003615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.30.30271270.26932385X-RAY DIFFRACTION87
2.3-2.4210.33391220.262475X-RAY DIFFRACTION92
2.421-2.57210.24261340.25782545X-RAY DIFFRACTION93
2.5721-2.76990.25541450.23562519X-RAY DIFFRACTION93
2.7699-3.04720.26781280.21882548X-RAY DIFFRACTION94
3.0472-3.48470.21891430.16762580X-RAY DIFFRACTION94
3.4847-4.37740.19381650.14992481X-RAY DIFFRACTION90
4.3774-16.80.17141300.14562567X-RAY DIFFRACTION93

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