3M7A | pdb_00003m7a

Crystal structure of Saro_0823 (YP_496102.1) a protein of unknown function from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.22 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3M7A/pdb

• Classification: structural genomics, unknown function
• Organism(s): Novosphingobium aromaticivorans DSM 12444
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-16 Released: 2010-04-21 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 
  0.148 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.117 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.119 (Depositor) 

Literature

Crystal structure of Saro_0823 (YP_496102.1) a protein of unknown function from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.22 A resolution

Joint Center for Structural Genomics (JCSG)

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 30.63 kDa 
• Atom Count: 2,753 
• Modeled Residue Count: 280 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A, B	140	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 0  Gene Names: Saro_0823
UniProt
Find proteins for Q2GA55 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore Q2GA55  Go to UniProtKB:  Q2GA55

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	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: 1.22 Å
• R-Value Free:  0.148 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.117 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.119 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33M7A

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.401	α = 90
b = 65.19	β = 128.6
c = 59.73	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-21 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-04-21
  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: 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