4E27 | pdb_00004e27

Crystal Structure of a Pentameric Capsid Protein Isolated from Metagenomic Phage Sequences Solved by Iodide SAD Phasing

• PDB DOI: https://doi.org/10.2210/pdb4E27/pdb

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


• Deposited: 2012-03-07 Released: 2013-03-27 
• 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: 2.40 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Crystal Structure of a Pentameric Capsid Protein Isolated from Metagenomic Phage Sequences Solved by Iodide SAD Phasing

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: 96.35 kDa 
• Atom Count: 6,174 
• Modeled Residue Count: 794 
• Deposited Residue Count: 875 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid Protein	A, B, C, D, E	175	unidentified	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	AA [auth D], BA [auth D], CA [auth D], DA [auth E], EA [auth E], F [auth A], FA [auth E], G [auth A], GA [auth E], H [auth A], HA [auth E], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], S [auth C], T [auth C], U [auth C], V [auth C], W [auth D], X [auth D], Y [auth D], Z [auth D]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
NA	R [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.71	α = 90
b = 68.36	β = 93.69
c = 107.83	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-27 
Deposition Author(s): Craig, T.K., Abendroth, J., Lorimer, D., Burgin Jr, A.B., Segall, A., Rohwer, F.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2015-04-01
  Changes: Derived calculations
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations