5TO2 | pdb_00005to2

Crystal structure of streptavidin with one wild type subunit and three mutated subunits (N23A/S27D/S45A)

PDB DOI: https://doi.org/10.2210/pdb5TO2/pdb

Classification: BIOTIN-BINDING PROTEIN
Organism(s): Streptomyces avidinii
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-10-16 Released: 2017-05-10
Deposition Author(s): Zhang, M., Biswas, S., Deng, W., Yu, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.234 (Depositor), 0.248 (DCC)
R-Value Work:
0.204 (Depositor)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5TO2

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of streptavidin with one wild type subunit and three mutated subunits (N23A/S27D/S45A)

Zhang, M., Biswas, S., Deng, W., Yu, H.

To be published.

Macromolecule Content

Total Structure Weight: 52.25 kDa
Atom Count: 3,907
Modeled Residue Count: 482
Deposited Residue Count: 499
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C	125	Streptomyces avidinii	Mutation(s): 3
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629 Go to UniProtKB: P22629
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22629
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	D	124	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629 Go to UniProtKB: P22629
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22629
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth D] MOL2 format, chain E [auth D] mmCIF format, chain E [auth D]	E [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth D] Interactions & Density Focus chain E [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.234 (Depositor), 0.248 (DCC)
R-Value Work: 0.204 (Depositor)
R-Value Observed: 0.206 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.357	α = 87.54
b = 56.738	β = 85.89
c = 57.435	γ = 67.99

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-05-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-05-10
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references

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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.