5HG2 | pdb_00005hg2

Backbone Modifications in the Protein GB1 Helix: beta-3-Ala24, beta-3-Lys28, beta-3-Lys31, beta-2-Asn35

PDB DOI: https://doi.org/10.2210/pdb5HG2/pdb

Classification: DE NOVO PROTEIN
Organism(s): Streptococcus sp. 'group G
Mutation(s): Yes

Deposited: 2016-01-07 Released: 2016-02-24
Deposition Author(s): Tavenor, N.A., Reinert, Z.E., Lengyel, G.A., Griffith, B.D., Horne, W.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.216 (Depositor), 0.217 (DCC)
R-Value Work:
0.199 (Depositor), 0.202 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Comparison of design strategies for alpha-helix backbone modification in a protein tertiary fold.

Tavenor, N.A., Reinert, Z.E., Lengyel, G.A., Griffith, B.D., Horne, W.S.

(2016) Chem Commun (Camb) 52: 3789-3792

PubMed: 26853882 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1039/c6cc00273k
Primary Citation Related Structures:
5HFY, 5HG2, 5HI1

PubMed Abstract:
We report here the comparison of five classes of unnatural amino acid building blocks for their ability to be accommodated into an α-helix in a protein tertiary fold context. High-resolution structural characterization and analysis of folding thermodynamics yield new insights into the relationship between backbone composition and folding energetics in α-helix mimetics and suggest refined design rules for engineering the backbones of natural sequences.

Organizational Affiliation

Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA. horne@pitt.edu.

Macromolecule Content

Total Structure Weight: 25.34 kDa
Atom Count: 2,066
Modeled Residue Count: 228
Deposited Residue Count: 228
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin G-binding protein G	A, B, C, D	57	Streptococcus sp. 'group G	Mutation(s): 1
UniProt
Find proteins for P19909 (Streptococcus sp. group G) Explore P19909 Go to UniProtKB: P19909
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19909
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth C] SDF format, chain G [auth D] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth C] MOL2 format, chain G [auth D] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth C] mmCIF format, chain G [auth D] mmCIF format, chain H [auth D]	E [auth A], F [auth C], G [auth D], H [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth C] Focus chain G [auth D] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth C] Focus chain G [auth D] Focus chain H [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth D] MOL2 format, chain I [auth D] mmCIF format, chain I [auth D]	I [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Interactions & Density Focus chain I [auth D]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
B2N Query on B2N	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₃		--
B3A Query on B3A	A, B, C, D	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
B3K Query on B3K	A, B, C, D	L-PEPTIDE LINKING	C₇ H₁₆ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.216 (Depositor), 0.217 (DCC)
R-Value Work: 0.199 (Depositor), 0.202 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.947	α = 90
b = 51.947	β = 90
c = 96.404	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-02-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM107161

Revision History (Full details and data files)

Version 1.0: 2016-02-24
Type: Initial release
Version 1.1: 2016-03-09
Changes: Database references
Version 1.2: 2016-07-27
Changes: Data collection
Version 1.3: 2017-09-13
Changes: Author supporting evidence, Derived calculations
Version 1.4: 2019-12-25
Changes: Author supporting evidence
Version 1.5: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations