5U2I | pdb_00005u2i

Crystal structure of a nucleoside diphosphate kinase from Naegleria fowleri

PDB DOI: https://doi.org/10.2210/pdb5U2I/pdb

Classification: TRANSFERASE
Organism(s): Naegleria fowleri
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-11-30 Released: 2017-01-25
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.169 (Depositor), 0.170 (DCC)
R-Value Work:
0.141 (Depositor), 0.141 (DCC)
R-Value Observed:
0.141 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a nucleoside diphosphate kinase from Naegleria fowleri

Conrady, D.G., Yano, J.K., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 107.02 kDa
Atom Count: 9,017
Modeled Residue Count: 911
Deposited Residue Count: 954
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A, B, C, D, E A, B, C, D, E, F	159	Naegleria fowleri	Mutation(s): 0 Gene Names: NF0036070 EC: 2.7.4.6
UniProt
Find proteins for A0A1S4NYF9 (Naegleria fowleri) Explore A0A1S4NYF9 Go to UniProtKB: A0A1S4NYF9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1S4NYF9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain V [auth F] SDF format, chain U [auth F] SDF format, chain S [auth E] SDF format, chain R [auth E] SDF format, chain P [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth D] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain V [auth F] MOL2 format, chain U [auth F] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] MOL2 format, chain P [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth D] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain V [auth F] mmCIF format, chain U [auth F] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E] mmCIF format, chain P [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A] H [auth B] I [auth B] K [auth C] L [auth D] G [auth A], H [auth B], I [auth B], K [auth C], L [auth D], P [auth D], R [auth E], S [auth E], U [auth F], V [auth F], W [auth F], X [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth F]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain T [auth E] SDF format, chain Q [auth D] SDF format, chain M [auth D] MOL2 format, chain T [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth D] mmCIF format, chain T [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth D]	M [auth D], Q [auth D], T [auth E]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Focus chain Q [auth D] Focus chain T [auth E] Interactions & Density Focus chain M [auth D] Focus chain Q [auth D] Focus chain T [auth E]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain J [auth B] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain J [auth B] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain J [auth B]	J [auth B], N [auth D], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain J [auth B] Focus chain N [auth D] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.169 (Depositor), 0.170 (DCC)
R-Value Work: 0.141 (Depositor), 0.141 (DCC)
R-Value Observed: 0.141 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.9	α = 90
b = 110.38	β = 118.55
c = 68.14	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MoRDa	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-01-25

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-01-25
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description