6NAB | pdb_00006nab

Crystal structure of prolyl-tRNA synthetase from Naegleria fowleri in complex with proline and adenosine monophophsphate (AMP)

PDB DOI: https://doi.org/10.2210/pdb6NAB/pdb

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

Deposited: 2018-12-05 Released: 2019-01-30
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.192 (Depositor), 0.190 (DCC)
R-Value Work:
0.151 (Depositor), 0.150 (DCC)
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 1.3 of the entry. See complete history.

Literature

Crystal structure of prolyl-tRNA synthetase from Naegleria fowleri in complex with proline and adenosine monophophsphate (AMP)

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

To be published.

Macromolecule Content

Total Structure Weight: 120.86 kDa
Atom Count: 8,938
Modeled Residue Count: 993
Deposited Residue Count: 1,026
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolyl-tRNA synthetase	A, B	513	Naegleria fowleri	Mutation(s): 0 EC: 6.1.1.15
UniProt
Find proteins for A0A4V8H034 (Naegleria fowleri) Explore A0A4V8H034 Go to UniProtKB: A0A4V8H034
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4V8H034
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain C [auth A]	C [auth A], M [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [auth B]
PRO Query on PRO Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain D [auth A] MOL2 format, chain N [auth B] MOL2 format, chain D [auth A] mmCIF format, chain N [auth B] mmCIF format, chain D [auth A]	D [auth A], N [auth B]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain D [auth A] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain N [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain E [auth A]	E [auth A], O [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.192 (Depositor), 0.190 (DCC)
R-Value Work: 0.151 (Depositor), 0.150 (DCC)
R-Value Observed: 0.152 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36nab

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.93	α = 90
b = 66.1	β = 102.03
c = 112.98	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
SIMBAD	phasing
PHASER	phasing
ARP/wARP	model building
Coot	model building
MoRDa	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2019-01-30
Type: Initial release
Version 1.1: 2020-01-15
Changes: Data collection
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-04-03
Changes: Refinement description