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- PDB-6che: Selenomethionine mutant (A34Sem) of protein GB1 examined by X-ray... -

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Basic information

Entry
Database: PDB / ID: 6che
TitleSelenomethionine mutant (A34Sem) of protein GB1 examined by X-ray diffraction
ComponentsImmunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / Immunoglobulin G-binding protein domain B1
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
IMIDAZOLE / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsChen, Q.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 P30 GM110758-02 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 P20 GM104316 United States
National Science Foundation (NSF, United States)MCB-1616178 United States
CitationJournal: J.Phys.Chem.B / Year: 2020
Title: 77Se NMR Probes the Protein Environment of Selenomethionine.
Authors: Chen, Q. / Xu, S. / Lu, X. / Boeri, M.V. / Pepelyayeva, Y. / Diaz, E.L. / Soni, S.D. / Allaire, M. / Forstner, M.B. / Bahnson, B.J. / Rozovsky, S.
History
DepositionFeb 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5674
Polymers6,2621
Non-polymers3053
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Mass spectrometry and SDS-PAGE gel were performed, as well as gel filtration chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)22.965, 37.048, 28.719
Angle α, β, γ (deg.)90.00, 110.16, 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: 6261.678 Da / Num. of mol.: 1 / Mutation: A34Sem
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. group G (bacteria) / Gene: spg / Cell line (production host): BL21DE3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19909
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.85 Å3/Da / Density % sol: 33.35 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 49% MPD 20% IPA 25 mM sodium acetate pH 4.9 20 mg/ml protein in 25 mM sodium acetate buffer pH 5.5 and 2 mM TCEP
PH range: 4.5-4.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 17, 2017
RadiationMonochromator: Asymmetric curved crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.1→26.96 Å / Num. obs: 18407 / % possible obs: 99.78 % / Redundancy: 2 % / Biso Wilson estimate: 6.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.02873 / Rpim(I) all: 0.02873 / Rrim(I) all: 0.04063 / Net I/σ(I): 11.55
Reflection shellResolution: 1.1→1.139 Å / Redundancy: 2 % / Rmerge(I) obs: 0.05434 / Num. unique obs: 1792 / CC1/2: 0.99 / Rpim(I) all: 0.05434 / Rrim(I) all: 0.07685 / % possible all: 98.79

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QMT

2qmt


Resolution: 1.1→26.959 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 12.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1471 3089 8.61 %
Rwork0.1293 --
obs0.1309 35896 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→26.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms437 0 21 97 555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007462
X-RAY DIFFRACTIONf_angle_d0.938625
X-RAY DIFFRACTIONf_dihedral_angle_d24.17161
X-RAY DIFFRACTIONf_chiral_restr0.07271
X-RAY DIFFRACTIONf_plane_restr0.00578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.11720.13361430.12071485X-RAY DIFFRACTION98
1.1172-1.13550.12271180.11751442X-RAY DIFFRACTION98
1.1355-1.15510.13161560.11231481X-RAY DIFFRACTION98
1.1551-1.17610.15671240.10991480X-RAY DIFFRACTION100
1.1761-1.19870.15871520.1191509X-RAY DIFFRACTION99
1.1987-1.22320.14191140.11781501X-RAY DIFFRACTION100
1.2232-1.24980.14141560.10691504X-RAY DIFFRACTION100
1.2498-1.27890.13711500.11511461X-RAY DIFFRACTION99
1.2789-1.31080.11631220.11991518X-RAY DIFFRACTION100
1.3108-1.34630.15041430.11191469X-RAY DIFFRACTION100
1.3463-1.38590.14531480.11241488X-RAY DIFFRACTION100
1.3859-1.43060.14141460.11911503X-RAY DIFFRACTION100
1.4306-1.48180.15331440.10681479X-RAY DIFFRACTION100
1.4818-1.54110.13611390.10791508X-RAY DIFFRACTION100
1.5411-1.61120.13721450.11321484X-RAY DIFFRACTION100
1.6112-1.69610.14941420.12421514X-RAY DIFFRACTION100
1.6961-1.80240.16611480.12951497X-RAY DIFFRACTION100
1.8024-1.94150.14271410.12961496X-RAY DIFFRACTION100
1.9415-2.13680.14191390.12231497X-RAY DIFFRACTION100
2.1368-2.44590.14181410.13811482X-RAY DIFFRACTION100
2.4459-3.08080.1761400.15441504X-RAY DIFFRACTION100
3.0808-26.96690.1461380.15461505X-RAY DIFFRACTION100

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