4JOS

Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Francisella philomiragia ATCC 25017 (Target NYSGRC-029335)

PDB DOI: https://doi.org/10.2210/pdb4JOS/pdb

Classification: HYDROLASE
Organism(s): Francisella philomiragia subsp. philomiragia ATCC 25017
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-03-18 Released: 2013-04-03
Deposition Author(s): Sampathkumar, P., Schramm, V.L., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.175
R-Value Work: 0.151
R-Value Observed: 0.152

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Francisella philomiragia ATCC 25017 (Target NYSGRC-029335)

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

To be published.

Macromolecule Content

Total Structure Weight: 56.62 kDa
Atom Count: 4,252
Modelled Residue Count: 458
Deposited Residue Count: 500
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteine nucleosidase	A, B	250	Francisella philomiragia subsp. philomiragia ATCC 25017	Mutation(s): 0 Gene Names: Fphi_0356 EC: 3.2.2.9
UniProt
Find proteins for B0TZL4 (Francisella philomiragia subsp. philomiragia (strain ATCC 25017 / FSC 153 / O#319-036)) Explore B0TZL4 Go to UniProtKB: B0TZL4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B0TZL4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADE Query on ADE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B]	C [auth A], G [auth B]	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	D [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

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: 1.45 Å
R-Value Free: 0.175
R-Value Work: 0.151
R-Value Observed: 0.152
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.747	α = 90
b = 74.937	β = 90
c = 114.542	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction
SCALEPACK	data scaling
SHELX	phasing
SHELXD	phasing
SHELXE	model building