3LM2 | pdb_00003lm2

Crystal structure of Putative kinase. (17743352) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3LM2/pdb

• Classification: TRANSFERASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-29 Released: 2010-02-23 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.186 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

Crystal structure of Putative kinase. (17743352) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 50.41 kDa 
• Atom Count: 3,911 
• Modeled Residue Count: 447 
• Deposited Residue Count: 452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative kinase	A, B	226	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: 17743352, AGR_L_95, Atu4836
UniProt
Find proteins for A9CH74 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CH74  Go to UniProtKB:  A9CH74

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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: 1.70 Å
• R-Value Free:  0.186 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33LM2

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.907	α = 97.98
b = 49.598	β = 104.64
c = 57.328	γ = 109.97

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-02-23
  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: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-27
  Changes: Data collection, Structure summary