5W5P | pdb_00005w5p

Crystal structure of Acinetobacter baumannii phage AM24 tailspike protein

PDB DOI: https://doi.org/10.2210/pdb5W5P/pdb

Classification: VIRAL PROTEIN
Organism(s): Acinetobacter phage AM24
Expression System: Escherichia coli B
Mutation(s): No

Deposited: 2017-06-15 Released: 2018-12-19
Deposition Author(s): Plattner, M., Shneider, M.M., Leiman, P.G.
Funding Organization(s): Ecole polytechnique federale de Lausanne

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free:
0.217 (Depositor), 0.225 (DCC)
R-Value Work:
0.180 (Depositor), 0.185 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5W5P

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

Literature

Crystal structure of Acinetobacter baumannii phage AM24 tailspike protein

Plattner, M., Shneider, M.M., Leiman, P.G.

To be published.

Macromolecule Content

Total Structure Weight: 67.47 kDa
Atom Count: 4,859
Modeled Residue Count: 610
Deposited Residue Count: 623
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail fiber protein	A	623	Acinetobacter phage AM24	Mutation(s): 0
UniProt
Find proteins for A0ACD6B8Y3 (Acinetobacter phage AM24) Explore A0ACD6B8Y3 Go to UniProtKB: A0ACD6B8Y3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8Y3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free: 0.217 (Depositor), 0.225 (DCC)
R-Value Work: 0.180 (Depositor), 0.185 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.657	α = 90
b = 100.657	β = 90
c = 307.836	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SHELXDE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-12-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Ecole polytechnique federale de Lausanne	Switzerland	0577-1

Revision History (Full details and data files)

Version 1.0: 2018-12-19
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Database references, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.