4XCQ | pdb_00004xcq

Clostridium botulinum phage c-st TubZ (C-terminal tail truncated protein)

• PDB DOI: https://doi.org/10.2210/pdb4XCQ/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium phage c-st
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-18 Released: 2016-03-09 
• Deposition Author(s): Oliva, M.A.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.239 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structure of phage c-st truncated TubZ at 2.4 Angstroms resolution

Oliva, M.A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 36.11 kDa 
• Atom Count: 2,454 
• Modeled Residue Count: 303 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TubZ	A	318	Clostridium phage c-st	Mutation(s): 0  Gene Names: CST189 EC: 3.6.5
UniProt
Find proteins for Q331T7 (Clostridium botulinum C phage) Explore Q331T7  Go to UniProtKB:  Q331T7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.239 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.97	α = 90
b = 86.342	β = 92.49
c = 44.734	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Oliva, M.A.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BFU2013-47014-P

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2016-07-13
  Changes: Data collection
• Version 1.2: 2016-12-14
  Changes: Other
• Version 2.0: 2017-09-13
  Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description