3R9L | pdb_00003r9l

Crystal structure of nucleoside diphosphate kinase from Giardia lamblia featuring a disordered dinucleotide binding site

PDB DOI: https://doi.org/10.2210/pdb3R9L/pdb

Classification: TRANSFERASE
Organism(s): Giardia lamblia ATCC 50803
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-03-25 Released: 2011-04-20
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.266 (Depositor), 0.260 (DCC)
R-Value Work:
0.234 (Depositor), 0.239 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of nucleoside diphosphate kinase from Giardia lamblia featuring a disordered dinucleotide binding site

Edwards, T.E., Gardberg, A.S., Sankaran, B., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 17.15 kDa
Atom Count: 827
Modeled Residue Count: 112
Deposited Residue Count: 155
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A	155	Giardia lamblia ATCC 50803	Mutation(s): 0 Gene Names: GL50803_11301 EC: 2.7.4.6
UniProt
Find proteins for A8BMG9 (Giardia intestinalis (strain ATCC 50803 / WB clone C6)) Explore A8BMG9 Go to UniProtKB: A8BMG9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8BMG9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.266 (Depositor), 0.260 (DCC)
R-Value Work: 0.234 (Depositor), 0.239 (DCC)
R-Value Observed: 0.236 (Depositor)

Diffraction Data:

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.96	α = 90
b = 116.96	β = 90
c = 62.69	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-04-20

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2011-04-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.