6NFE | pdb_00006nfe

Crystal Structure of Ribose-phosphate Pyrophosphokinase from Legionella pneumophila with bound AMP, ADP, and Ribose-5-Phosphate

PDB DOI: https://doi.org/10.2210/pdb6NFE/pdb

Classification: LIGASE
Organism(s): Legionella pneumophila
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-12-19 Released: 2019-01-02
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.176 (Depositor), 0.185 (DCC)
R-Value Work:
0.152 (Depositor)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal Structure of Ribose-phosphate Pyrophosphokinase from Legionella pneumophila with bound AMP, ADP, and Ribose-5-Phosphate

Bolejack, M.J., Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 73.23 kDa
Atom Count: 5,318
Modeled Residue Count: 597
Deposited Residue Count: 646
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose-phosphate pyrophosphokinase	A, B	323	Legionella pneumophila	Mutation(s): 0 Gene Names: prsA, prs, C3927_02005, NCTC12024_00599 EC: 2.7.6.1
UniProt
Find proteins for Q5ZY30 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZY30 Go to UniProtKB: Q5ZY30
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ZY30
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain P [auth B] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] mmCIF format, chain N [auth A] mmCIF format, chain P [auth B]	N [auth A], P [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain N [auth A] Focus chain P [auth B] Interactions & Density Focus chain N [auth A] Focus chain P [auth B]
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A]	H [auth A], J [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain J [auth A]
HSX Query on HSX Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain T [auth B] MOL2 format, chain E [auth A] MOL2 format, chain T [auth B] mmCIF format, chain E [auth A] mmCIF format, chain T [auth B]	E [auth A], T [auth B]	5-O-phosphono-alpha-D-ribofuranose C₅ H₁₁ O₈ P KTVPXOYAKDPRHY-AIHAYLRMSA-N		Interactions Focus chain E [auth A] Focus chain T [auth B] Interactions & Density Focus chain E [auth A] Focus chain T [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain V [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain V [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain V [auth B]	C [auth A] F [auth A] I [auth A] K [auth A] L [auth A] C [auth A], F [auth A], I [auth A], K [auth A], L [auth A], M [auth A], O [auth A], Q [auth B], R [auth B], S [auth B], V [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth B]
EOH Query on EOH Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth A] SDF format, chain U [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain U [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain U [auth B]	D [auth A], G [auth A], U [auth B]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth A] Focus chain U [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth A] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.176 (Depositor), 0.185 (DCC)
R-Value Work: 0.152 (Depositor)
R-Value Observed: 0.152 (Depositor)

Diffraction Data:

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109	α = 90
b = 109	β = 90
c = 97.3	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-01-02

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2019-01-02
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary