4DNH | pdb_00004dnh

Crystal structure of hypothetical protein SMc04132 from Sinorhizobium meliloti 1021

• PDB DOI: https://doi.org/10.2210/pdb4DNH/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-08 Released: 2012-03-28 
• Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Seidel, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.240 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.174 (Depositor) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Crystal structure of hypothetical protein SMc04132 from Sinorhizobium meliloti 1021

Malashkevich, V.N., Bhosle, R., Toro, R., Seidel, R., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 44.07 kDa 
• Atom Count: 3,067 
• Modeled Residue Count: 386 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	396	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: NP_384226.1, R00120, SMc04132
UniProt
Find proteins for Q92T60 (Rhizobium meliloti (strain 1021)) Explore Q92T60  Go to UniProtKB:  Q92T60

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: 2.50 Å
• R-Value Free:  0.240 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.174 (Depositor) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.291	α = 90
b = 75.291	β = 90
c = 139.518	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-28 
Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Seidel, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-03-28
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary