3BDR

Crystal structure of fatty acid-binding protein-like Ycf58 from Thermosynecoccus elongatus. Northeast Structural Genomics Consortium target TeR13.

PDB DOI: https://doi.org/10.2210/pdb3BDR/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Synechococcus elongatus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-15 Released: 2007-11-27
Deposition Author(s): Kuzin, A.P., Su, M., Seetharaman, J., Forouhar, F., Wang, D., Janjua, H., Cunningham, K., Ma, L.-C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.262
R-Value Work: 0.236
R-Value Observed: 0.236

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of fatty acid-binding protein-like Ycf58 from Thermosynecoccus elongatus.

Kuzin, A.P., Su, M., Seetharaman, J., Forouhar, F., Wang, D., Janjua, H., Cunningham, K., Ma, L.-C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 21.97 kDa
Atom Count: 1,231
Modelled Residue Count: 156
Deposited Residue Count: 190
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ycf58 protein	A	190	Synechococcus elongatus	Mutation(s): 0 Gene Names: ycf58, tll1699
UniProt
Find proteins for Q8DI91 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DI91 Go to UniProtKB: Q8DI91
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DI91
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		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: 2.80 Å
R-Value Free: 0.262
R-Value Work: 0.236
R-Value Observed: 0.236
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.014	α = 90
b = 75.014	β = 90
c = 83.359	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-11-27

Deposition Author(s):

Seetharaman, J.

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-11-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Database references, Structure summary

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 R01GM133198.