3MPD | pdb_00003mpd

Crystal structure of nucleoside diphosphate kinase from encephalitozoon cuniculi, cubic form, apo

PDB DOI: https://doi.org/10.2210/pdb3MPD/pdb

Classification: TRANSFERASE
Organism(s): Encephalitozoon cuniculi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-04-26 Released: 2010-05-12
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.207 (Depositor), 0.223 (DCC)
R-Value Work:
0.175 (Depositor), 0.190 (DCC)
R-Value Observed:
0.177 (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 encephalitozoon cuniculi

Gardberg, A., Edwards, T.E., Staker, B., SSGCID

To be published.

Macromolecule Content

Total Structure Weight: 34.02 kDa
Atom Count: 2,566
Modeled Residue Count: 294
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A, B	151	Encephalitozoon cuniculi	Mutation(s): 0 Gene Names: ECU06_1530, HM-1:IMSS, NDK1 EC: 2.7.4.6
UniProt
Find proteins for Q8SRM7 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRM7 Go to UniProtKB: Q8SRM7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8SRM7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.207 (Depositor), 0.223 (DCC)
R-Value Work: 0.175 (Depositor), 0.190 (DCC)
R-Value Observed: 0.177 (Depositor)

Diffraction Data:

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.33	α = 90
b = 111.33	β = 90
c = 111.33	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-05-12

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2010-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
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.