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)

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)

wwPDB Validation 3D Report Full Report

Validation slider image for 1Z2Z

This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8Q0M2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-04-26

Deposition Author(s):

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.