4E27

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.256
R-Value Work: 0.202
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 96.35 kDa
Atom Count: 6,174
Modelled Residue Count: 794
Deposited Residue Count: 875
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid Protein	A, B, C, D, E	175	unidentified	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain F [auth A] SDF format, chain FA [auth E] SDF format, chain G [auth A] SDF format, chain GA [auth E] SDF format, chain H [auth A] SDF format, chain HA [auth E] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth E] EA [auth E] 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		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain F [auth A] Focus chain FA [auth E] Focus chain G [auth A] Focus chain GA [auth E] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain F [auth A] Focus chain FA [auth E] Focus chain G [auth A] Focus chain GA [auth E] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B]	R [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.256
R-Value Work: 0.202
R-Value Observed: 0.205
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-03-27

Deposition Author(s):

Revision History (Full details and data files)

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