3KDR

The Crystal Structure of a HK97 Family Phage Portal Protein from Corynebacterium diphtheriae to 2.9A

• PDB DOI: https://doi.org/10.2210/pdb3KDR/pdb

• Classification: structural genomics, unknown function
• Organism(s): Corynebacterium diphtheriae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-23 Released: 2009-12-29 
• Deposition Author(s): Nocek, B., Stein, A.J., Mulligan, R., Duggan, E., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.245 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

The Crystal Structure of a HK97 Family Phage Portal Protein from Corynebacterium diphtheriae to 2.9A

Nocek, B., Stein, A.J., Mulligan, R., Duggan, E., Abdullah, J., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C12  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Biological Assembly 2  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 72-mer - A72 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 72-mer - A72 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 100.37 kDa 
• Atom Count: 6,311 
• Modelled Residue Count: 855 
• Deposited Residue Count: 930 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HK97 Family Phage Portal Protein	A, B, C	310	Corynebacterium diphtheriae	Mutation(s): 0  Gene Names: DIP1825
UniProt
Find proteins for Q6NFR1 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NFR1  Go to UniProtKB:  Q6NFR1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth B], I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	D [auth A], H [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.245 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 340.068	α = 90
b = 340.068	β = 90
c = 340.068	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing
BUCCANEER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-29 
Deposition Author(s): Nocek, B., Stein, A.J., Mulligan, R., Duggan, E., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description