2QSK | pdb_00002qsk

Atomic-resolution crystal structure of the Recombinant form of Scytovirin

• PDB DOI: https://doi.org/10.2210/pdb2QSK/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Scytonema varium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-07-31 Released: 2007-11-27 
• Deposition Author(s): Moulaei, T., Botos, I., Ziolkowska, N.E., Dauter, Z., Wlodawer, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.147 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.128 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.129 (Depositor) 

Starting Model: experimental

Literature

Atomic-resolution crystal structure of the antiviral lectin scytovirin.

Moulaei, T., Botos, I., Ziolkowska, N.E., Bokesch, H.R., Krumpe, L.R., McKee, T.C., O'Keefe, B.R., Dauter, Z., Wlodawer, A.

(2007) Protein Sci 16: 2756-2760

• PubMed: 17965185 
• DOI: https://doi.org/10.1110/ps.073157507
• Primary Citation of Related Structures:  
  2QSK, 2QT4


• PubMed Abstract: 
  

  The crystal structures of the natural and recombinant antiviral lectin scytovirin (SVN) were solved by single-wavelength anomalous scattering and refined with data extending to 1.3 A and 1.0 A resolution, respectively. A molecule of SVN consists of a single chain 95 amino acids long, with an almost perfect sequence repeat that creates two very similar domains (RMS deviation 0.25 A for 40 pairs of Calpha atoms). The crystal structure differs significantly from a previously published NMR structure of the same protein, with the RMS deviations calculated separately for the N- and C-terminal domains of 5.3 A and 3.7 A, respectively, and a very different relationship between the two domains. In addition, the disulfide bonding pattern of the crystal structures differs from that described in the previously published mass spectrometry and NMR studies.

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Organizational Affiliation: 
• Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, NCI-Frederick, Frederick, Maryland 21702-1201, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.93 kDa 
• Atom Count: 859 
• Modeled Residue Count: 95 
• Deposited Residue Count: 95 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
scytovirin	A	95	Scytonema varium	Mutation(s): 0
UniProt
Find proteins for P86041 (Scytonema varium) Explore P86041  Go to UniProtKB:  P86041

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.147 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.128 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.129 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.2	α = 90
b = 38.79	β = 90
c = 59.87	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-27 
Deposition Author(s): Moulaei, T., Botos, I., Ziolkowska, N.E., Dauter, Z., Wlodawer, A.

Revision History  

• Version 1.0: 2007-11-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary