2I6D | pdb_00002i6d

The structure of a putative RNA methyltransferase of the TrmH family from Porphyromonas gingivalis.

PDB DOI: https://doi.org/10.2210/pdb2I6D/pdb

Classification: TRANSFERASE
Organism(s): Porphyromonas gingivalis W83
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-08-28 Released: 2006-10-17
Deposition Author(s): Cuff, M.E., Mussar, K.E., Li, H., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.235 (Depositor), 0.232 (DCC)
R-Value Work:
0.189 (Depositor), 0.187 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

The structure of a putative RNA methyltransferase of the TrmH family from Porphyromonas gingivalis.

Cuff, M.E., Mussar, K.E., Li, H., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 28.45 kDa
Atom Count: 2,332
Modeled Residue Count: 251
Deposited Residue Count: 257
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA methyltransferase, TrmH family	A	257	Porphyromonas gingivalis W83	Mutation(s): 6 Gene Names: SpoU, PG_0744 EC: 2.1.1
UniProt
Find proteins for Q7MW92 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MW92 Go to UniProtKB: Q7MW92
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7MW92
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.235 (Depositor), 0.232 (DCC)
R-Value Work: 0.189 (Depositor), 0.187 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.921	α = 90
b = 107.119	β = 90
c = 120.352	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-10-17

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2006-10-17
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2024-11-13
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.