3H02 | pdb_00003h02

2.15 Angstrom Resolution Crystal Structure of Naphthoate Synthase from Salmonella typhimurium.

• PDB DOI: https://doi.org/10.2210/pdb3H02/pdb

• Classification: LYASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-08 Released: 2009-04-21 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.215 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

2.15 Angstrom Resolution Crystal Structure of Naphthoate Synthase from Salmonella typhimurium.

Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 196 kDa 
• Atom Count: 13,009 
• Modeled Residue Count: 1,557 
• Deposited Residue Count: 1,728 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Naphthoate synthase	A, B, C, D, E, F	288	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: menB, STM2307 EC: 4.1.3.36
UniProt
Find proteins for Q7CQ56 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q7CQ56  Go to UniProtKB:  Q7CQ56

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], M [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BCT	H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], N [auth F], O [auth F]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.215 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33h02

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.897	α = 90
b = 132.819	β = 90
c = 151.791	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary