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- PDB-5hg2: Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, be... -

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Basic information

Entry
Database: PDB / ID: 5hg2
TitleBackbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-2-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: 1.8 Å
AuthorsTavenor, N.A. / Reinert, Z.E. / Lengyel, G.A. / Griffith, B.D. / Horne, W.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107161 United States
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 1.2Jul 27, 2016Group: Data collection
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
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

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G
B: Immunoglobulin G-binding protein G
C: Immunoglobulin G-binding protein G
D: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3449
Polymers24,9514
Non-polymers3935
Water4,882271
1
A: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3302
Polymers6,2381
Non-polymers921
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
3
C: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3302
Polymers6,2381
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4464
Polymers6,2381
Non-polymers2083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.947, 51.947, 96.404
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 6237.776 Da / Num. of mol.: 4 / Fragment: UNP residues 302-357 / Source method: obtained synthetically / Source: (synth.) Streptococcus sp. group G (bacteria) / References: UniProt: P19909
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsBackbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-2-Asn35

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 0.1 M magnesium acetate, 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 RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinType: pseudo-merohedral / Operator: h,-k,-l / Fraction: 0.27
ReflectionResolution: 1.8→51.95 Å / Num. obs: 22477 / % possible obs: 95 % / Redundancy: 13.25 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 25.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 13.18 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 4.9 / % possible all: 90.5

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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: 1.8→51.947 Å / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 31.63 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2165 2007 8.94 %
Rwork0.1994 --
obs0.2026 22438 94.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→51.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 25 271 2052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061817
X-RAY DIFFRACTIONf_angle_d1.132465
X-RAY DIFFRACTIONf_dihedral_angle_d14.203555
X-RAY DIFFRACTIONf_chiral_restr0.041288
X-RAY DIFFRACTIONf_plane_restr0.004309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8009-1.84590.56561400.65741390X-RAY DIFFRACTION82
1.8459-1.89580.52381280.48821356X-RAY DIFFRACTION82
1.8958-1.95160.35161400.36961378X-RAY DIFFRACTION81
1.9516-2.01460.27641380.2991368X-RAY DIFFRACTION81
2.0146-2.08660.29151360.25381381X-RAY DIFFRACTION82
2.0866-2.17010.29021330.23671386X-RAY DIFFRACTION82
2.1701-2.26880.23391320.22271412X-RAY DIFFRACTION85
2.2688-2.38840.25111410.20691495X-RAY DIFFRACTION89
2.3884-2.5380.23311460.19231530X-RAY DIFFRACTION91
2.538-2.73390.19771470.19381562X-RAY DIFFRACTION91
2.7339-3.00890.20351480.17791515X-RAY DIFFRACTION91
3.0089-3.4440.18631540.17421556X-RAY DIFFRACTION91
3.444-4.33790.15361510.14841552X-RAY DIFFRACTION91
4.3379-35.34080.18351510.1711550X-RAY DIFFRACTION91

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