2NYU | pdb_00002nyu

Crystal Structure of Human FtsJ homolog 2 (E.coli) protein in complex with S-adenosylmethionine

PDB DOI: https://doi.org/10.2210/pdb2NYU/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-11-21 Released: 2006-12-05
Deposition Author(s): Dong, A., Wu, H., Zeng, H., Loppnau, P., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.281 (Depositor), 0.275 (DCC)
R-Value Work:
0.226 (Depositor), 0.224 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2NYU

Ligand Structure Quality Assessment

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

Literature

The Crystal Structure of Human FtsJ homolog 2 (E.coli) protein in complex with AdoMet

Wu, H., Dong, A., Zeng, H., Loppnau, P., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N.

To be published.

Macromolecule Content

Total Structure Weight: 44.22 kDa
Atom Count: 3,042
Modeled Residue Count: 363
Deposited Residue Count: 392
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ribosomal RNA methyltransferase 2	A, B	196	Homo sapiens	Mutation(s): 1 Gene Names: FTSJ2, FJH1 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UI43 (Homo sapiens) Explore Q9UI43 Go to UniProtKB: Q9UI43
PHAROS: Q9UI43 GTEx: ENSG00000122687
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UI43
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.281 (Depositor), 0.275 (DCC)
R-Value Work: 0.226 (Depositor), 0.224 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.022	α = 90
b = 102.022	β = 90
c = 37.068	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
JDirector	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-12-05

Deposition Author(s):

Arrowsmith, C.H.

Plotnikov, A.N.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2006-12-05
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2021-10-20
Changes: Database references, Derived calculations
Version 1.5: 2023-08-30
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.