2AZ3 | pdb_00002az3

Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum in complex with CDP

PDB DOI: https://doi.org/10.2210/pdb2AZ3/pdb

Classification: TRANSFERASE
Organism(s): Halobacterium salinarum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-09-09 Released: 2005-12-20
Deposition Author(s): Besir, H., Zeth, K., Bracher, A., Heider, U., Ishibashi, M., Tokunaga, M., Oesterhelt, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.271 (Depositor), 0.205 (DCC)
R-Value Work:
0.200 (Depositor), 0.206 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum

Besir, H., Zeth, K., Bracher, A., Heider, U., Ishibashi, M., Tokunaga, M., Oesterhelt, D.

(2005) FEBS Lett 579: 6595-6600

PubMed: 16293253 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2005.10.052
Primary Citation Related Structures:
2AZ1, 2AZ3

PubMed Abstract:
Nucleoside diphosphate kinase from the halophilic archaeon Halobacterium salinarum was crystallized in a free state and a substrate-bound form with CDP. The structures were solved to a resolution of 2.35 and 2.2A, respectively. Crystals with the apo-form were obtained with His6-tagged enzyme, whereas the untagged form was used for co-crystallization with the nucleotide. Crosslinking under different salt and pH conditions revealed a stronger oligomerization tendency for the tagged protein at low and high salt concentrations. The influence of the His6-tag on the halophilic nature of the enzyme is discussed on the basis of the observed structural properties.

Organizational Affiliation

Max-Planck-Institut für Biochemie, Abteilung Membranbiochemie, Am Klopferspitz 18, 82152 Martinsried, Germany. hbesir@biochem.mpg.de

Macromolecule Content

Total Structure Weight: 169 kDa
Atom Count: 11,117
Modeled Residue Count: 1,367
Deposited Residue Count: 1,476
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, G, H, I	164	Halobacterium salinarum	Mutation(s): 0 Gene Names: ndk EC: 2.7.4.6
UniProt
Find proteins for P61136 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)) Explore P61136 Go to UniProtKB: P61136
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61136
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDP Query on CDP Download:Ideal Coordinates CCD File SDF format, chain T [auth I] SDF format, chain S [auth H] SDF format, chain R [auth G] SDF format, chain Q [auth F] SDF format, chain P [auth E] SDF format, chain O [auth D] SDF format, chain N [auth C] SDF format, chain M [auth B] SDF format, chain K [auth A] MOL2 format, chain T [auth I] MOL2 format, chain S [auth H] MOL2 format, chain R [auth G] MOL2 format, chain Q [auth F] MOL2 format, chain P [auth E] MOL2 format, chain O [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] mmCIF format, chain T [auth I] mmCIF format, chain S [auth H] mmCIF format, chain R [auth G] mmCIF format, chain Q [auth F] mmCIF format, chain P [auth E] mmCIF format, chain O [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A]	K [auth A] M [auth B] N [auth C] O [auth D] P [auth E] K [auth A], M [auth B], N [auth C], O [auth D], P [auth E], Q [auth F], R [auth G], S [auth H], T [auth I]	CYTIDINE-5'-DIPHOSPHATE C₉ H₁₅ N₃ O₁₁ P₂ ZWIADYZPOWUWEW-XVFCMESISA-N		Interactions Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth G] Focus chain S [auth H] Focus chain T [auth I] Interactions & Density Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth G] Focus chain S [auth H] Focus chain T [auth I]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A]	J [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Interactions & Density Focus chain J [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.271 (Depositor), 0.205 (DCC)
R-Value Work: 0.200 (Depositor), 0.206 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.37	α = 90
b = 71.52	β = 95.53
c = 157.99	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-12-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-12-20
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description