6RTQ | pdb_00006rtq

Hoefavidin P61C mutant generates a stabilized octamer

PDB DOI: https://doi.org/10.2210/pdb6RTQ/pdb

Classification: BIOTIN BINDING PROTEIN
Organism(s): Hoeflea phototrophica DFL-43
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-05-26 Released: 2019-08-14
Deposition Author(s): Livnah, O., Avraham, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.283 (Depositor), 0.294 (DCC)
R-Value Work:
0.227 (Depositor), 0.239 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Generating a High Valency Biotin Binder by Selecting Uniform Protein Assemblies via Crystallization

Avraham, O., Levi-Kalisman, Y., Livnah, O.

(2019) Crystals (Basel)

DOI: https://doi.org/10.3390/cryst9070353

Macromolecule Content

Total Structure Weight: 31.16 kDa
Atom Count: 2,073
Modeled Residue Count: 266
Deposited Residue Count: 292
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hoefavidin	A, B	146	Hoeflea phototrophica DFL-43	Mutation(s): 1 Gene Names: HPDFL43_17171
UniProt
Find proteins for A9D857 (Hoeflea phototrophica (strain DSM 17068 / NCIMB 14078 / DFL-43)) Explore A9D857 Go to UniProtKB: A9D857
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9D857
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.283 (Depositor), 0.294 (DCC)
R-Value Work: 0.227 (Depositor), 0.239 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.885	α = 90
b = 81.885	β = 90
c = 130.429	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-08-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-08-14
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.