4DMI | pdb_00004dmi

Crystal Structure of a Pentameric Capsid Protein Isolated from Metagenomic Phage Sequences (CASP)

• PDB DOI: https://doi.org/10.2210/pdb4DMI/pdb

• Classification: VIRAL PROTEIN
• Organism(s): unidentified
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-07 Released: 2012-08-29 
• Deposition Author(s): Craig, T.K., Abendroth, J., Lorimer, D., Burgin Jr, A.B., Segall, A., Rohwer, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.182 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Literature

Crystal Structure of a Pentameric Capsid Protein Isolated from Metagenomic Phage Sequences

Craig, T.K., Abendroth, J., Lorimer, D., Burgin Jr, A.B., Segall, A., Rohwer, F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 93.41 kDa 
• Atom Count: 7,494 
• Modeled Residue Count: 840 
• Deposited Residue Count: 880 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid Protein	A, B, C, D, E	176	unidentified	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	F [auth A], I [auth C], J [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	G [auth A], H [auth B], K [auth C], L [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.182 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.57	α = 90
b = 147.87	β = 112.05
c = 57.85	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Craig, T.K., Abendroth, J., Lorimer, D., Burgin Jr, A.B., Segall, A., Rohwer, F.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations