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- PDB-6cpz: Selenomethionine mutant (I6Sem) of protein GB1 examined by X-ray ... -

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Basic information

Entry
Database: PDB / ID: 6cpz
TitleSelenomethionine mutant (I6Sem) 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
PHOSPHATE ION / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsChen, Q. / Rozovsky, S.
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
DepositionMar 14, 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 1.2Jul 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,29210
Polymers12,4392
Non-polymers8538
Water3,225179
1
A: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6465
Polymers6,2201
Non-polymers4264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6465
Polymers6,2201
Non-polymers4264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.890, 36.489, 48.940
Angle α, β, γ (deg.)90.00, 98.67, 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: 6219.598 Da / Num. of mol.: 2 / Mutation: I6Sem
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. group G (bacteria) / Gene: spg / Cell line (production host): BL21(DE3) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19909
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: 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
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 1.99 Å3/Da / Density % sol: 38.32 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 48% MPD 20% IPA 25 mM sodium acetate buffer pH 4.7 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: Asymetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.12→27.571 Å / Num. obs: 69779 / % possible obs: 97.43 % / Redundancy: 2 % / Biso Wilson estimate: 7.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.01784 / Rpim(I) all: 0.01784 / Rrim(I) all: 0.02524 / Net I/σ(I): 12.98
Reflection shellResolution: 1.12→1.16 Å

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Processing

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

2qmt


Resolution: 1.12→27.571 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1561 3802 5.45 %
Rwork0.1369 --
obs0.1379 69779 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.12→27.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms868 0 52 179 1099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008970
X-RAY DIFFRACTIONf_angle_d1.0811327
X-RAY DIFFRACTIONf_dihedral_angle_d20.938349
X-RAY DIFFRACTIONf_chiral_restr0.086150
X-RAY DIFFRACTIONf_plane_restr0.006161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.13420.16171340.12682320X-RAY DIFFRACTION91
1.1342-1.14910.16111420.1182431X-RAY DIFFRACTION92
1.1491-1.16490.1471390.12252349X-RAY DIFFRACTION92
1.1649-1.18150.13771320.12052340X-RAY DIFFRACTION92
1.1815-1.19920.1581340.12952378X-RAY DIFFRACTION92
1.1992-1.21790.16881390.12662391X-RAY DIFFRACTION92
1.2179-1.23790.18341330.11762352X-RAY DIFFRACTION94
1.2379-1.25920.15151370.11722431X-RAY DIFFRACTION93
1.2592-1.28210.15171380.11982422X-RAY DIFFRACTION95
1.2821-1.30680.14351450.1112427X-RAY DIFFRACTION94
1.3068-1.33340.13051400.11452431X-RAY DIFFRACTION94
1.3334-1.36240.15141380.12192391X-RAY DIFFRACTION93
1.3624-1.39410.1681430.11632478X-RAY DIFFRACTION94
1.3941-1.4290.12651320.1182360X-RAY DIFFRACTION94
1.429-1.46760.17271430.11432465X-RAY DIFFRACTION95
1.4676-1.51080.14711400.11212409X-RAY DIFFRACTION96
1.5108-1.55960.13381370.10822511X-RAY DIFFRACTION96
1.5596-1.61530.15511400.11422447X-RAY DIFFRACTION96
1.6153-1.680.15661480.12322474X-RAY DIFFRACTION96
1.68-1.75640.15361450.13482537X-RAY DIFFRACTION97
1.7564-1.8490.19051450.13912512X-RAY DIFFRACTION98
1.849-1.96480.13781450.1332486X-RAY DIFFRACTION98
1.9648-2.11650.12431430.13012523X-RAY DIFFRACTION98
2.1165-2.32940.13111460.14462514X-RAY DIFFRACTION98
2.3294-2.66620.1781530.15822532X-RAY DIFFRACTION99
2.6662-3.35820.16631470.16132548X-RAY DIFFRACTION99
3.3582-27.57910.18031440.1622518X-RAY DIFFRACTION98

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