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- PDB-5hfy: Backbone Modifications in the Protein GB1 Helix: beta-2-Ala24, be... -

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Basic information

Entry
Database: PDB / ID: 5hfy
TitleBackbone Modifications in the Protein GB1 Helix: beta-2-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35
ComponentsImmunoglobulin G-binding protein G
KeywordsDE NOVO PROTEIN / synthetic protein
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
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTavenor, N.A. / Reinert, Z.E. / Lengyel, G.A. / Griffith, B.D. / Horne, W.S.
CitationJournal: Chem.Commun.(Camb.) / Year: 2016
Title: Comparison of design strategies for alpha-helix backbone modification in a protein tertiary fold.
Authors: Tavenor, N.A. / Reinert, Z.E. / Lengyel, G.A. / Griffith, B.D. / Horne, W.S.
History
DepositionJan 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _struct_conn.pdbx_leaving_atom_flag

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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)12,4762
Polymers12,4762
Non-polymers00
Water2,162120
1
A: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,2381
Polymers6,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,2381
Polymers6,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.816, 22.415, 65.261
Angle α, β, γ (deg.)90.00, 134.09, 90.00
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: 6237.775 Da / Num. of mol.: 2 / Fragment: UNP residues 302-357 / Source method: obtained synthetically / Source: (synth.) Streptococcus sp. group G (bacteria) / References: UniProt: P19909
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsBackbone Modifications in the Protein GB1 Helix: beta-2-Ala24, beta-3-Lys28, beta-3-Lys31, beta-3-Asn35

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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: 1.95 Å3/Da / Density % sol: 37.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.2 M sodium acetate pH 4.6, 20% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→23.44 Å / Num. obs: 7188 / % possible obs: 97.8 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 18.5
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 3.6 / % possible all: 90.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QMT

2qmt


Resolution: 1.95→23.435 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 25.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 712 9.92 %
Rwork0.1954 --
obs0.199 7179 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→23.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 0 120 1000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005910
X-RAY DIFFRACTIONf_angle_d1.0431240
X-RAY DIFFRACTIONf_dihedral_angle_d14.531282
X-RAY DIFFRACTIONf_chiral_restr0.042145
X-RAY DIFFRACTIONf_plane_restr0.003160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.10050.25481320.21991201X-RAY DIFFRACTION92
2.1005-2.31170.26991380.20371267X-RAY DIFFRACTION97
2.3117-2.64580.27031430.22831305X-RAY DIFFRACTION100
2.6458-3.33190.22911460.20581315X-RAY DIFFRACTION100
3.3319-23.43670.1981530.16881379X-RAY DIFFRACTION100

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