3CEC | pdb_00003cec

Crystal structure of a putative antidote protein of plasmid maintenance system (npun_f2943) from nostoc punctiforme pcc 73102 at 1.60 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3CEC/pdb

• Classification: TRANSCRIPTION
• Organism(s): Nostoc punctiforme PCC 73102
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-28 Released: 2008-03-11 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.202 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Crystal structure of putative antidote protein of plasmid maintenance system (ZP_00107635.1) from Nostoc punctiforme PCC 73102 at 1.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 12.11 kDa 
• Atom Count: 892 
• Modeled Residue Count: 91 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative antidote protein of plasmid maintenance system	A	104	Nostoc punctiforme PCC 73102	Mutation(s): 0  Gene Names: ZP_00107635.1
UniProt
Find proteins for D0VWT6 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102)) Explore D0VWT6  Go to UniProtKB:  D0VWT6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	B [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.202 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33CEC

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.07	α = 90
b = 36.71	β = 98.38
c = 50.05	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-11 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-03-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary