2QG3 | pdb_00002qg3

CRYSTAL STRUCTURE OF A TYW3 METHYLTRANSFERASE-LIKE PROTEIN (AF_2059) FROM ARCHAEOGLOBUS FULGIDUS DSM 4304 AT 1.95 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb2QG3/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Archaeoglobus fulgidus DSM 4304
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-06-28 Released: 2007-07-17
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.253 (Depositor), 0.261 (DCC)
R-Value Work:
0.199 (Depositor), 0.206 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2QG3

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of uncharacterized protein AF2059 (2648472) from Archaeoglobus fulgidus at 1.95 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 47.61 kDa
Atom Count: 2,971
Modeled Residue Count: 384
Deposited Residue Count: 416
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0130 protein AF_2059	A, B	208	Archaeoglobus fulgidus DSM 4304	Mutation(s): 4 Gene Names: 2648472, AF_2059 EC: 2.1.1.282
UniProt
Find proteins for O28220 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28220 Go to UniProtKB: O28220
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O28220
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: 1.95 Å
R-Value Free: 0.253 (Depositor), 0.261 (DCC)
R-Value Work: 0.199 (Depositor), 0.206 (DCC)
R-Value Observed: 0.201 (Depositor)

Diffraction Data:

Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.334	α = 90
b = 59.334	β = 90
c = 109.102	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
XSCALE	data scaling
PDB_EXTRACT	data extraction
SHARP	phasing
Blu-Ice	data collection
XDS	data reduction
SHELXD	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-07-17

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-07-17
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-11-20
Changes: Data collection, Refinement description, 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.