3MT1 | pdb_00003mt1

Crystal structure of putative carboxynorspermidine decarboxylase protein from Sinorhizobium meliloti

• PDB DOI: https://doi.org/10.2210/pdb3MT1/pdb

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


• Deposited: 2010-04-29 Released: 2010-06-30 
• Deposition Author(s): Chang, C., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.256 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.190 (Depositor) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of putative carboxynorspermidine decarboxylase protein from Sinorhizobium meliloti

Chang, C., 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)

Macromolecule Content 

• Total Structure Weight: 83.5 kDa 
• Atom Count: 5,523 
• Modeled Residue Count: 694 
• Deposited Residue Count: 730 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative carboxynorspermidine decarboxylase protein	A, B	365	Sinorhizobium meliloti	Mutation(s): 0  Gene Names: nspC, RB1551, SM_b21631, SMb21631 EC: 4.1.1 (PDB Primary Data), 4.1.1.96 (UniProt)
UniProt
Find proteins for Q92TG9 (Rhizobium meliloti (strain 1021)) Explore Q92TG9  Go to UniProtKB:  Q92TG9

Small Molecules

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

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: 2.50 Å
• R-Value Free:  0.256 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.190 (Depositor) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.769	α = 90
b = 75.773	β = 90
c = 129.801	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-30 
Deposition Author(s): Chang, C., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary