3BFM | pdb_00003bfm

Crystal structure of a biotin protein ligase-like protein of unknown function (tm1040_0394) from silicibacter sp. tm1040 at 1.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3BFM/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Ruegeria sp. TM1040
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-11-21 Released: 2007-12-04 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Crystal structure of biotin protein ligase-like protein of unknown function (YP_612389.1) from Silicibacter sp. TM1040 at 1.70 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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.88 kDa 
• Atom Count: 1,925 
• Modeled Residue Count: 230 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biotin protein ligase-like protein of unknown function	A	235	Ruegeria sp. TM1040	Mutation(s): 0  Gene Names: YP_612389.1, TM1040_0394

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PE	D [auth A]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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: 1.70 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33BFM

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.76	α = 90
b = 36.56	β = 99.28
c = 71	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-04 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-12-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary