6AAC

Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with mAzZLys


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.479 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with mAzZLys

Yanagisawa, T.KUratani, M.Yokoyama, S.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyrrolysine--tRNA ligase
A
274Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)Mutation(s): 2 
Gene Names: pylS
EC: 6.1.1.26
Find proteins for Q8PWY1 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Go to UniProtKB:  Q8PWY1
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ATP
Query on ATP

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Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
9TR
Query on 9TR

Download SDF File 
Download CCD File 
A
N6-{[(3-azidophenyl)methoxy]carbonyl}-L-lysine
C14 H19 N5 O4
HFCHIMDWTVTIEA-LBPRGKRZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.479 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.141 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.492α = 90.00
b = 44.284β = 118.49
c = 72.637γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan24550203

Revision History 

  • Version 1.0: 2019-04-17
    Type: Initial release