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- PDB-6lji: X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11V -

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Basic information

Entry
Database: PDB / ID: 6lji
TitleX-ray structure of synthetic GB1 domain with mutations K10(DVA), T11V
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: 1.843 Å
AuthorsPenmatsa, A. / Chatterjee, J. / Majumder, P. / Khatri, B.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)EMR/2016/006193 India
Department of Science & Technology (DST, 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
DepositionDec 16, 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G
B: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)12,3072
Polymers12,3072
Non-polymers00
Water52229
1
A: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,1541
Polymers6,1541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,1541
Polymers6,1541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.722, 23.066, 48.395
Angle α, β, γ (deg.)90.000, 109.040, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 6153.654 Da / Num. of mol.: 2 / Fragment: GB1 domain / Mutation: K10(DVA), T11V / Source method: obtained synthetically / Source: (synth.) Streptococcus sp. group G (bacteria) / References: UniProt: P06654
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.94 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG 4000, 0.1M MES pH 6.0

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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: Jul 30, 2019 / Details: Osmic mirros
RadiationMonochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→38.09 Å / Num. obs: 8079 / % possible obs: 96 % / Redundancy: 4 % / Biso Wilson estimate: 17.64 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02 / Rpim(I) all: 0.011 / Rrim(I) all: 0.023 / Net I/σ(I): 36.3 / Num. measured all: 32240
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
1.84-1.883.20.05713024020.9980.0360.06813.878.9
9.03-38.093.30.012798410.0060.01245.695.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QMT

2qmt


Resolution: 1.843→23.636 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 45.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3281 392 4.87 %
Rwork0.278 7653 -
obs0.2805 8045 94.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.49 Å2 / Biso mean: 20.9694 Å2 / Biso min: 8.96 Å2
Refinement stepCycle: final / Resolution: 1.843→23.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms864 0 0 29 893
Biso mean---25.22 -
Num. residues----112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006876
X-RAY DIFFRACTIONf_angle_d0.7431196
X-RAY DIFFRACTIONf_chiral_restr0.045144
X-RAY DIFFRACTIONf_plane_restr0.003154
X-RAY DIFFRACTIONf_dihedral_angle_d15.361502
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8432-2.10980.39891170.3216242591
2.1098-2.65750.35181400.3128255396
2.6575-23.6360.29431350.2481267597

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