3LLV

The Crystal Structure of the NAD(P)-binding domain of an Exopolyphosphatase-related protein from Archaeoglobus fulgidus to 1.7A

• PDB DOI: https://doi.org/10.2210/pdb3LLV/pdb

• Classification: NAD(P) binding protein
• Organism(s): Archaeoglobus fulgidus DSM 4304
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-29 Released: 2010-02-09 
• Deposition Author(s): Stein, A.J., Chang, C., Weger, A., Hendricks, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.235 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

The Crystal Structure of the NAD(P)-binding domain of an Exopolyphosphatase-related protein from Archaeoglobus fulgidus to 1.7A

Stein, A.J., Chang, C., Weger, A., Hendricks, R., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.66 kDa 
• Atom Count: 1,075 
• Modelled Residue Count: 133 
• Deposited Residue Count: 141 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exopolyphosphatase-related protein	A	141	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0  Gene Names: AF_2029
UniProt
Find proteins for O28250 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28250  Go to UniProtKB:  O28250

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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:  0.235 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.994	α = 90
b = 39.994	β = 90
c = 295.489	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-09 
Deposition Author(s): Stein, A.J., Chang, C., Weger, A., Hendricks, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-02-09
  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: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary