2F46 | pdb_00002f46

Crystal structure of a putative phosphatase (nma1982) from neisseria meningitidis z2491 at 1.41 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2F46/pdb

• Classification: HYDROLASE
• Organism(s): Neisseria meningitidis Z2491
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-11-22 Released: 2006-02-07 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 
  0.228 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 A resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases.

Krishna, S.S., Tautz, L., Xu, Q., McMullan, D., Miller, M.D., Abdubek, P., Ambing, E., Astakhova, T., Axelrod, H.L., Carlton, D., Chiu, H.J., Clayton, T., DiDonato, M., Duan, L., Elsliger, M.A., Grzechnik, S.K., Hale, J., Hampton, E., Han, G.W., Haugen, J., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Koesema, E., Morse, A.T., Mustelin, T., Nigoghossian, E., Oommachen, S., Reyes, R., Rife, C.L., van den Bedem, H., Weekes, D., White, A., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2007) Proteins 69: 415-421

• PubMed: 17636569 
• DOI: https://doi.org/10.1002/prot.21314
• Primary Citation of Related Structures:  
  2F46

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Organizational Affiliation: 
• Burnham Institute for Medical Research, La Jolla, California, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.88 kDa 
• Atom Count: 2,866 
• Modeled Residue Count: 286 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein	A, B	156	Neisseria meningitidis Z2491	Mutation(s): 3  Gene Names: 7380613
UniProt
Find proteins for A1KVD0 (Neisseria meningitidis serogroup C / serotype 2a (strain ATCC 700532 / DSM 15464 / FAM18)) Explore A1KVD0  Go to UniProtKB:  A1KVD0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNL	E [auth B]	Unknown ligand VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free:  0.228 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32F46

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.278	α = 90
b = 33.466	β = 96.18
c = 59.899	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-07 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-02-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary