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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.235
R-Value Work: 0.210
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O28250
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.210
R-Value Observed: 0.212
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-02-09

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.