1Z2Z | pdb_00001z2z

Crystal Structure of the Putative tRNA pseudouridine synthase D (TruD) from Methanosarcina mazei, Northeast Structural Genomics Target MaR1

• PDB DOI: https://doi.org/10.2210/pdb1Z2Z/pdb

• Classification: LYASE
• Organism(s): Methanosarcina mazei
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-03-10 Released: 2005-04-26 
• Deposition Author(s): Forouhar, F., Yong, W., Ciano, M., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.296 (Depositor), 0.306 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

Crystal Structure of the Putative tRNA pseudouridine synthase D (TruD) from Methanosarcina mazei, Northeast Structural Genomics Target MaR1

Forouhar, F., Yong, W., Ciano, M., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 102.12 kDa 
• Atom Count: 7,176 
• Modelled Residue Count: 874 
• Deposited Residue Count: 892 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable tRNA pseudouridine synthase D	A, B	446	Methanosarcina mazei	Mutation(s): 9  Gene Names: truD EC: 4.2.1.70 (PDB Primary Data), 5.4.99.27 (UniProt)
UniProt
Find proteins for Q8Q0M2 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8Q0M2  Go to UniProtKB:  Q8Q0M2

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.296 (Depositor), 0.306 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.562	α = 90
b = 132.531	β = 116.98
c = 66.779	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-26 
Deposition Author(s): Forouhar, F., Yong, W., Ciano, M., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2005-04-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary