3LZK | pdb_00003lzk

The crystal structure of a probably aromatic amino acid degradation proteiN from Sinorhizobium meliloti 1021

• PDB DOI: https://doi.org/10.2210/pdb3LZK/pdb

• Classification: HYDROLASE
• Organism(s): Sinorhizobium meliloti
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-03-01 Released: 2010-03-16 
• Deposition Author(s): Tan, K., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.227 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

The crystal structure of a probably aromatic amino acid degradation protein from Sinorhizobium meliloti 1021

Tan, K., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A.

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 157.14 kDa 
• Atom Count: 10,754 
• Modeled Residue Count: 1,362 
• Deposited Residue Count: 1,436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fumarylacetoacetate hydrolase family protein	A, B, C, D	359	Sinorhizobium meliloti	Mutation(s): 0  Gene Names: R02938, SMc03207
UniProt
Find proteins for Q92LT4 (Rhizobium meliloti (strain 1021)) Explore Q92LT4  Go to UniProtKB:  Q92LT4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth B], G [auth C], H [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A, B, C, D	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.227 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.773	α = 90
b = 188.894	β = 115.17
c = 67.736	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-16 
Deposition Author(s): Tan, K., Xu, X., Cui, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary