4L0M

Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Borrelia burgdorferi B31 bound to Adenine (Target NYSGRC-029268 )

PDB DOI: https://doi.org/10.2210/pdb4L0M/pdb

Classification: HYDROLASE
Organism(s): Borreliella burgdorferi B31
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-05-31 Released: 2013-08-14
Deposition Author(s): Sampathkumar, P., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.267
R-Value Work: 0.227
R-Value Observed: 0.229

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Borrelia burgdorferi B31 bound to Adenine (Target NYSGRC-029268 )

Sampathkumar, P., Ahmed, M., Attonito, J., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Eromenok, G., Fiser, A., Glenn, A.S., Hammonds, J., Himmel, D.M., Hillerich, B., Khafizov, K., Lafleur, J., Love, J.D., Stead, M., Seidel, R., Toro, R., Morisco, L.L., Sojitra, S.S., Wasserman, S.R., Haapalainen, A., Suarez, J., Schramm, V.L., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 29.55 kDa
Atom Count: 2,047
Modelled Residue Count: 237
Deposited Residue Count: 259
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase	A	259	Borreliella burgdorferi B31	Mutation(s): 0 Gene Names: BB_0375, BB_0375 pfs gene product, pfs EC: 3.2.2.16 (PDB Primary Data), 3.2.2.9 (PDB Primary Data)
UniProt
Find proteins for O50162 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31)) Explore O50162 Go to UniProtKB: O50162
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O50162
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADE Query on ADE Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-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: 1.70 Å
R-Value Free: 0.267
R-Value Work: 0.227
R-Value Observed: 0.229
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.083	α = 90
b = 48.083	β = 90
c = 241.838	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
XDS	data reduction
Aimless	data scaling
SHELX	phasing
SHELXD	phasing
SHELXE	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-08-14

Deposition Author(s):

Sampathkumar, P.

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-08-14
Type: Initial release
Version 1.1: 2013-11-27
Changes: Structure summary
Version 1.2: 2017-11-15
Changes: Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.