6USM | pdb_00006usm

Structure of nuclease domain of human parvovirus B19 non-structural protein 1 in complex with zinc

• PDB DOI: https://doi.org/10.2210/pdb6USM/pdb

• Classification: REPLICATION
• Organism(s): Escherichia coli, Human parvovirus B19
• Expression System: Expression vector pET-mod
• Mutation(s): No 


• Deposited: 2019-10-28 Released: 2020-12-09 
• Deposition Author(s): Tewary, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.37 Å
• R-Value Free: 
  0.296 (DCC) 
• R-Value Work: 
  0.248 (DCC) 

Starting Model: other

Literature

B19 Parvovirus Non-structural protein 1 in complex with zinc

Tewary, S.K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 60.69 kDa 
• Atom Count: 4,190 
• Modeled Residue Count: 532 
• Deposited Residue Count: 542 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin-binding protein	A	371	Escherichia coli	Mutation(s): 0  Gene Names: malE
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein NS1	B	171	Human parvovirus B19	Mutation(s): 0  Gene Names: NS EC: 3.6.4.12
UniProt
Find proteins for Q6TV13 (Human parvovirus B19) Explore Q6TV13  Go to UniProtKB:  Q6TV13

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	C	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.37 Å
• R-Value Free:  0.296 (DCC) 
• R-Value Work:  0.248 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.69	α = 90
b = 102.69	β = 90
c = 134.21	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Tewary, S.K.

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2024-04-03
  Changes: Refinement description