1YX2 | pdb_00001yx2

Crystal Structure of the Probable Aminomethyltransferase from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb1YX2/pdb

Classification: TRANSFERASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2005-02-19 Released: 2005-04-05
Deposition Author(s): Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.288 (Depositor), 0.287 (DCC)
R-Value Work:
0.212 (Depositor), 0.211 (DCC)
R-Value Observed:
0.219 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1YX2

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

Literature

Crystal Structure of the Probable Aminomethyltransferase from Bacillus subtilis

Kim, Y., Quartey, P., Lezondra, L., Collart, F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 80.95 kDa
Atom Count: 6,482
Modeled Residue Count: 720
Deposited Residue Count: 730
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminomethyltransferase	A, B	365	Bacillus subtilis	Mutation(s): 7 Gene Names: gcvT EC: 2.1.2.10
UniProt
Find proteins for P54378 (Bacillus subtilis (strain 168)) Explore P54378 Go to UniProtKB: P54378
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54378
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

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: 2.08 Å
R-Value Free: 0.288 (Depositor), 0.287 (DCC)
R-Value Work: 0.212 (Depositor), 0.211 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.628	α = 90
b = 88.095	β = 101.78
c = 88.764	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
SHARP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-04-05

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2005-04-05
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: 2024-11-06
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.