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- PDB-6l9b: X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11A -

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Basic information

Entry
Database: PDB / ID: 6l9b
TitleX-ray structure of synthetic GB1 domain with mutations K10(DVA), T11A
ComponentsImmunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / Synthetic GB1 domain variant / D-aminoacid substitution
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 / 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
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPenmatsa, A. / Chatterjee, J. / Khatri, B. / Majumder, P.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Science & Technology (India)EMR/2016/006193 India
Department of Science & Technology (India)IR/SO/LU/0003/2010-PHASE-II India
CitationJournal: Chem Sci / Year: 2020
Title: Increasing protein stability by engineering the n -> pi * interaction at the beta-turn.
Authors: Khatri, B. / Majumder, P. / Nagesh, J. / Penmatsa, A. / Chatterjee, J.
History
DepositionNov 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.identifier_ORCID
Revision 1.2Feb 9, 2022Group: Database references / Category: citation / database_2
Item: _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,1261
Polymers6,1261
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3600 Å2
Unit cell
Length a, b, c (Å)43.771, 43.771, 48.099
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-116-

HOH

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Components

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


Mass: 6125.601 Da / Num. of mol.: 1 / Mutation: K10(DVA), T11A / Source method: obtained synthetically / Source: (synth.) Streptococcus sp. group G (bacteria) / References: UniProt: P06654
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.35 % / Description: Flat rod like crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M CaCl2, 0.1M sodium acetate (pH 4.6), 30% Isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 16, 2018
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.948→37.91 Å / Num. obs: 3909 / % possible obs: 94.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 26.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.032 / Rrim(I) all: 0.099 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-27.10.36114802080.9630.1310.3863.865.4
8.49-37.917.40.04498670.9990.0150.04326.698.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
Aimless0.5.21data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QMT
Resolution: 1.95→37.907 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.03
RfactorNum. reflection% reflection
Rfree0.2498 219 5.61 %
Rwork0.2063 --
obs0.209 3901 93.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.86 Å2 / Biso mean: 30.1944 Å2 / Biso min: 15.68 Å2
Refinement stepCycle: final / Resolution: 1.95→37.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms432 0 0 16 448
Biso mean---36.24 -
Num. residues----56
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007438
X-RAY DIFFRACTIONf_angle_d0.831597
X-RAY DIFFRACTIONf_chiral_restr0.04771
X-RAY DIFFRACTIONf_plane_restr0.00577
X-RAY DIFFRACTIONf_dihedral_angle_d13.943252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-2.0180.3391920.2318174290
2.4547-37.9070.22941270.198194097

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