3NA2 | pdb_00003na2

Crystal Structure of Protein of Unknown Function from Mine Drainage Metagenome Leptospirillum rubarum

• PDB DOI: https://doi.org/10.2210/pdb3NA2/pdb

• Classification: Structural Genomics, Unknown function
• Organism(s): Leptospirillum rubarum
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-05-31 Released: 2010-07-28 
• Deposition Author(s): Kim, Y., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.248 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Crsystal Structure of Protein of Unknown Function from Mine Drainage Metagenome Leptospirillum rubarum

Kim, Y., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A.

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 79.05 kDa 
• Atom Count: 4,516 
• Modeled Residue Count: 537 
• Deposited Residue Count: 688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D	172	Leptospirillum rubarum	Mutation(s): 0  Gene Names: UBAL2_80620259
UniProt
Find proteins for A0A059XTK7 (Leptospirillum ferriphilum YSK) Explore A0A059XTK7  Go to UniProtKB:  A0A059XTK7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	F [auth A], H [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACY	E [auth A], G [auth D]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.248 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.367	α = 90
b = 115.047	β = 90
c = 73.596	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
RESOLVE	model building
SOLVE	phasing
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Kim, Y., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary