2NMM | pdb_00002nmm

Crystal structure of human phosphohistidine phosphatase. Northeast Structural Genomics Consortium target HR1409

• PDB DOI: https://doi.org/10.2210/pdb2NMM/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-10-22 Released: 2007-01-23 
• Deposition Author(s): Kuzin, A.P., Abashidze, M., Forouhar, F., Seetharaman, J., Kent, C., Fang, Y., Cunningham, K., Conover, K., Ma, L.C., Xiao, R., Acton, T., Montelione, G., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.261 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of human phosphohistidine phosphatase. Northeast Structural Genomics Consortium target HR1409

Kuzin, A.P., Abashidze, M., Forouhar, F., Seetharaman, J., Kent, C., Fang, Y., Cunningham, K., Conover, K., Ma, L.C., Xiao, R., Acton, T., Montelione, G., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PQS (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.42 kDa 
• Atom Count: 2,707 
• Modeled Residue Count: 334 
• Deposited Residue Count: 405 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14 kDa phosphohistidine phosphatase	A, B, C	135	Homo sapiens	Mutation(s): 3  Gene Names: PHPT1, PHP14 EC: 3.1.3 (PDB Primary Data), 3.9.1.3 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRX4 (Homo sapiens) Explore Q9NRX4  Go to UniProtKB:  Q9NRX4
GTEx:  ENSG00000054148

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth B], G [auth B], H [auth C], I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.261 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.685	α = 90
b = 60.088	β = 90
c = 79.299	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-23 
Deposition Author(s): Kuzin, A.P., Abashidze, M., Forouhar, F., Seetharaman, J., Kent, C., Fang, Y., Cunningham, K., Conover, K., Ma, L.C., Xiao, R., Acton, T., Montelione, G., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2007-01-23
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Structure summary