3FLJ | pdb_00003flj

Crystal structure of uncharacterized protein conserved in bacteria with a cystatin-like fold (YP_168589.1) from SILICIBACTER POMEROYI DSS-3 at 2.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3FLJ/pdb

• Classification: structural genomics, unknown function
• Organism(s): Ruegeria pomeroyi DSS-3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-18 Released: 2009-01-13 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.185 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Crystal structure of uncharacterized protein conserved in bacteria with a cystatin-like fold (YP_168589.1) from SILICIBACTER POMEROYI DSS-3 at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

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: 18.1 kDa 
• Atom Count: 1,267 
• Modeled Residue Count: 141 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein conserved in bacteria with a cystatin-like fold	A	155	Ruegeria pomeroyi DSS-3	Mutation(s): 0  Gene Names: SPO3393, YP_168589.1
UniProt
Find proteins for Q5LN19 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LN19  Go to UniProtKB:  Q5LN19

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNL	B [auth A]	Unknown ligand

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: 2.00 Å
• R-Value Free:  0.185 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33FLJ

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.88	α = 90
b = 120.88	β = 90
c = 120.88	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
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-13 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-01-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary