3A1M | pdb_00003a1m

A fusion protein of a beta helix region of gene product 5 and the foldon region of bacteriophage T4

PDB DOI: https://doi.org/10.2210/pdb3A1M/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Tequatrovirus T4
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-04-11 Released: 2010-04-21
Deposition Author(s): Yokoi, N., Suzuki, A., Hikage, T., Koshiyama, T., Terauchi, M., Yutani, K., Kanamaru, S., Arisaka, F., Yamane, T., Watanabe, Y., Ueno, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.268 (Depositor), 0.260 (DCC)
R-Value Work:
0.223 (Depositor), 0.214 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

Literature

Construction of Robust Bio-nanotubes using the Controlled Self-Assembly of Component Proteins of Bacteriophage T4

Yokoi, N., Inaba, H., Terauchi, M., Stieg, A.Z., Sanghamitra, N.J., Koshiyama, T., Yutani, K., Kanamaru, S., Arisaka, F., Hikage, T., Suzuki, A., Yamane, T., Gimzewski, J.K., Watanabe, Y., Kitagawa, S., Ueno, T.

(2010) Small 6: 1873-1879

PubMed: 20661999 Search on PubMed
DOI: https://doi.org/10.1002/smll.201000772
Primary Citation Related Structures:
3A1M

Organizational Affiliation

Department of Chemistry, Graduate School of Science, Nagoya university, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.

Macromolecule Content

Total Structure Weight: 89.18 kDa
Atom Count: 4,820
Modeled Residue Count: 590
Deposited Residue Count: 834
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
chimera of thrombin cleavage site, Tail-associated lysozyme, Fibritin	A, B, C, D, E A, B, C, D, E, F	139	Tequatrovirus T4	Mutation(s): 1 EC: 3.2.1.17
UniProt
Find proteins for P10104 (Enterobacteria phage T4) Explore P10104 Go to UniProtKB: P10104
Find proteins for P16009 (Enterobacteria phage T4) Explore P16009 Go to UniProtKB: P16009
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P10104 P16009
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth D]	G [auth A], H [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.268 (Depositor), 0.260 (DCC)
R-Value Work: 0.223 (Depositor), 0.214 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.814	α = 90
b = 57.01	β = 103.9
c = 136.594	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-04-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-04-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-06-28
Changes: Source and taxonomy
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-11-01
Changes: Data collection, Refinement description