2O2X | pdb_00002o2x

Crystal structure of a putative had-like phosphatase (mll2559) from mesorhizobium loti at 1.50 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2O2X/pdb

• Classification: HYDROLASE
• Organism(s): Mesorhizobium loti
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-11-30 Released: 2006-12-19 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.167 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Literature

Crystal structure of hypothetical protein (NP_103874.1) from Mesorhizobium loti at 1.50 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 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.75 kDa 
• Atom Count: 1,940 
• Modeled Residue Count: 209 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein	A	218	Mesorhizobium loti	Mutation(s): 6  Gene Names: NP_103874.1 EC: 3.1.3.82
UniProt
Find proteins for Q98I56 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q98I56  Go to UniProtKB:  Q98I56

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.50 Å
• R-Value Free:  0.167 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32O2X

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.48	α = 90
b = 66.27	β = 108.53
c = 41.02	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-19 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-12-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Data collection, Structure summary