3O31 | pdb_00003o31

E81Q mutant of MtNAS in complex with a reaction intermediate

PDB DOI: https://doi.org/10.2210/pdb3O31/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Methanothermobacter thermautotrophicus str. Delta H
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-07-23 Released: 2011-06-08
Deposition Author(s): Dreyfus, C., Pignol, D., Arnoux, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.233 (Depositor), 0.233 (DCC)
R-Value Work:
0.188 (Depositor), 0.187 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The crystallographic structure of thermoNicotianamine synthase with a synthetic reaction intermediate highlights the sequential processing mechanism.

Dreyfus, C., Larrouy, M., Cavelier, F., Martinez, J., Pignol, D., Arnoux, P.

(2011) Chem Commun (Camb) 47: 5825-5827

PubMed: 21487608 Search on PubMed
DOI: https://doi.org/10.1039/c1cc10565e
Primary Citation Related Structures:
3O31

PubMed Abstract:
We determined the three-dimensional structure of a complex between an archaeal nicotianamine synthase homologue and a chemically synthesised reaction intermediate. This structure suggests that the enzymes cavity allows both an ordered substrate binding and provides energetic coupling of the reaction intermediate formation and translocation.

Organizational Affiliation

Laboratoire de Bioénergétique Cellulaire - Institut de Biologie Environnementale et Biotechnologie, Commissariat à l'Energie Atomique-UMR 6191 Biologie Végétale et Microbiologie Environnementale, Centre National de la Recherche Scientifique, 13115 Saint-Paul-lez-Durance, France.

Macromolecule Content

Total Structure Weight: 68.18 kDa
Atom Count: 5,223
Modeled Residue Count: 528
Deposited Residue Count: 592
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ThermoNicotianamine Synthase	A, B	296	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 1 Gene Names: MTH675, MTH_675
UniProt
Find proteins for O26771 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26771 Go to UniProtKB: O26771
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O26771
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3O3 Query on 3O3 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	N-[(3S)-3-amino-3-carboxypropyl]-L-glutamic acid C₉ H₁₆ N₂ O₆ VTEXNADNTYNYRI-WDSKDSINSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] I [auth B] D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.233 (Depositor), 0.233 (DCC)
R-Value Work: 0.188 (Depositor), 0.187 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.37	α = 90
b = 67.899	β = 90
c = 147.408	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-06-08

Deposition Author(s):

Dreyfus, C.

Pignol, D.

Arnoux, P.

Revision History (Full details and data files)

Version 1.0: 2011-06-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-11-12
Changes: Structure summary
Version 1.3: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary