3JU2 | pdb_00003ju2

CRYSTAL STRUCTURE OF PROTEIN SMc04130 FROM Sinorhizobium meliloti 1021

• PDB DOI: https://doi.org/10.2210/pdb3JU2/pdb

• Classification: structural genomics, unknown function
• Organism(s): Sinorhizobium meliloti
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-14 Released: 2009-09-22 
• Deposition Author(s): Patskovsky, Y., Foti, R., Ramagopal, U., Malashkevich, V., Toro, R., Freeman, J., Miller, S., Sauder, J.M., Raushel, F.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.246 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

CRYSTAL STRUCTURE OF PROTEIN SMc04130 FROM Sinorhizobium meliloti

Patskovsky, Y., Foti, R., Ramagopal, U., Malashkevich, V., Freeman, J., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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: 30.9 kDa 
• Atom Count: 2,327 
• Modeled Residue Count: 275 
• Deposited Residue Count: 284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein SMc04130	A	284	Sinorhizobium meliloti	Mutation(s): 0  Gene Names: R00122, SMc04130
UniProt
Find proteins for Q92T58 (Rhizobium meliloti (strain 1021)) Explore Q92T58  Go to UniProtKB:  Q92T58

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.246 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.102	α = 90
b = 92.102	β = 90
c = 157.345	γ = 120

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Patskovsky, Y., Foti, R., Ramagopal, U., Malashkevich, V., Toro, R., Freeman, J., Miller, S., Sauder, J.M., Raushel, F.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references