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- PDB-5hi1: Backbone Modifications in the Protein GB1 Helix: Aib24, beta-3-Ly... -

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Basic information

Entry
Database: PDB / ID: 5hi1
TitleBackbone Modifications in the Protein GB1 Helix: Aib24, beta-3-Lys28, beta-3-Lys31, Aib35
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
ACETATE ION / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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 11, 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 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 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 2.0Nov 15, 2023Group: Atomic model / Data collection
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_rmsd_angle / pdbx_validate_torsion
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

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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
E: Immunoglobulin G-binding protein G
F: Immunoglobulin G-binding protein G
G: Immunoglobulin G-binding protein G
H: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,67610
Polymers49,5588
Non-polymers1182
Water4,774265
1
A: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,1951
Polymers6,1951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,1951
Polymers6,1951
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)6,2542
Polymers6,1951
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2542
Polymers6,1951
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,1951
Polymers6,1951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,1951
Polymers6,1951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,1951
Polymers6,1951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,1951
Polymers6,1951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.371, 73.430, 79.436
Angle α, β, γ (deg.)90.00, 99.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-217-

HOH

21C-228-

HOH

31E-138-

HOH

41F-132-

HOH

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Components

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


Mass: 6194.751 Da / Num. of mol.: 8 / Fragment: UNP residues 302-357 / Source method: obtained synthetically / Source: (synth.) Streptococcus sp. group G (bacteria) / References: UniProt: P19909
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsBackbone Modifications in the Protein GB1 Helix: Aib24, beta-3-Lys28, beta-3-Lys31, Aib35

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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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1M sodium acetate pH 4.5, 20% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→41.15 Å / Num. obs: 22880 / % possible obs: 99.2 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 15.9
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.04 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 4.2 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QMT

2qmt


Resolution: 2.15→41.15 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.64 / Phase error: 25.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 2000 8.75 %
Rwork0.2141 --
obs0.2174 22864 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.83 Å2
Refinement stepCycle: LAST / Resolution: 2.15→41.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 8 265 3757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083572
X-RAY DIFFRACTIONf_angle_d1.0744886
X-RAY DIFFRACTIONf_dihedral_angle_d20.2091142
X-RAY DIFFRACTIONf_chiral_restr0.066562
X-RAY DIFFRACTIONf_plane_restr0.004613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20380.34971320.26881380X-RAY DIFFRACTION92
2.2038-2.26340.28511400.27061464X-RAY DIFFRACTION97
2.2634-2.32990.30991420.26231483X-RAY DIFFRACTION100
2.3299-2.40510.30051430.25431488X-RAY DIFFRACTION100
2.4051-2.49110.33191460.24281518X-RAY DIFFRACTION100
2.4911-2.59080.28751400.25451462X-RAY DIFFRACTION100
2.5908-2.70870.2921440.24381510X-RAY DIFFRACTION100
2.7087-2.85150.27531430.24071497X-RAY DIFFRACTION100
2.8515-3.03010.26171430.21981489X-RAY DIFFRACTION100
3.0301-3.2640.22411460.21491517X-RAY DIFFRACTION100
3.264-3.59230.23661420.19871488X-RAY DIFFRACTION100
3.5923-4.11160.24361460.17951514X-RAY DIFFRACTION100
4.1116-5.17860.1721440.16821517X-RAY DIFFRACTION100
5.1786-41.16090.24121490.19831537X-RAY DIFFRACTION99

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