4J4B | pdb_00004j4b

PylD in complex with L-lysine-Ne-D-ornithine and NADH

PDB DOI: https://doi.org/10.2210/pdb4J4B/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methanosarcina barkeri str. Fusaro
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-02-06 Released: 2013-06-12
Deposition Author(s): Quitterer, F., Beck, P., Bacher, A., Groll, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.205 (Depositor), 0.205 (DCC)
R-Value Observed:
0.207 (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

Structure and Reaction Mechanism of Pyrrolysine Synthase (PylD).

Quitterer, F., Beck, P., Bacher, A., Groll, M.

(2013) Angew Chem Int Ed Engl 52: 7033-7037

PubMed: 23720358 Search on PubMed
DOI: https://doi.org/10.1002/anie.201301164
Primary Citation Related Structures:
4J43, 4J49, 4J4B, 4J4H, 4JK3

Organizational Affiliation

Center for Integrated Protein Science Munich at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany.

Macromolecule Content

Total Structure Weight: 57.7 kDa
Atom Count: 4,239
Modeled Residue Count: 518
Deposited Residue Count: 518
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PylD	A, B	259	Methanosarcina barkeri str. Fusaro	Mutation(s): 0 Gene Names: Mbar_A0835 EC: 1.4.1
UniProt
Find proteins for Q46E80 (Methanosarcina barkeri (strain Fusaro / DSM 804)) Explore Q46E80 Go to UniProtKB: Q46E80
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q46E80
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
0TF Query on 0TF Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth B]	N~6~-D-ornithyl-L-lysine C₁₁ H₂₄ N₄ O₃ AOOVWOOUTNDWMA-BDAKNGLRSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.205 (Depositor), 0.205 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.383	α = 90
b = 142.44	β = 90
c = 167.305	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
PHASER	phasing
REFMAC	refinement
PROTEUM PLUS	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-06-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-06-12
Type: Initial release
Version 1.1: 2013-07-10
Changes: Database references
Version 1.2: 2024-04-03
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary

4J4B | pdb_00004j4b

PylD in complex with L-lysine-Ne-D-ornithine and NADH

Literature

Structure and Reaction Mechanism of Pyrrolysine Synthase (PylD).

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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