4FVS | pdb_00004fvs

Crystal structure of a putative lipoprotein (BDI_3050) from Parabacteroides distasonis ATCC 8503 at 2.70 A resolution

PDB DOI: https://doi.org/10.2210/pdb4FVS/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Parabacteroides distasonis ATCC 8503
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-06-29 Released: 2012-07-25
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.224 (Depositor), 0.230 (DCC)
R-Value Work:
0.187 (Depositor), 0.200 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a putative lipoprotein (BDI_3050) from Parabacteroides distasonis ATCC 8503 at 2.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 148.34 kDa
Atom Count: 10,531
Modeled Residue Count: 1,283
Deposited Residue Count: 1,290
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 lipoprotein	A, B, C, D, E A, B, C, D, E, F	215	Parabacteroides distasonis ATCC 8503	Mutation(s): 0 Gene Names: BDI_3050
UniProt
Find proteins for A6LGE3 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LGE3 Go to UniProtKB: A6LGE3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6LGE3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain H [auth C] SDF format, chain I [auth D] SDF format, chain J [auth F] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] MOL2 format, chain I [auth D] MOL2 format, chain J [auth F] mmCIF format, chain G [auth C] mmCIF format, chain H [auth C] mmCIF format, chain I [auth D] mmCIF format, chain J [auth F]	G [auth C], H [auth C], I [auth D], J [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth C] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth F] Interactions & Density Focus chain G [auth C] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.224 (Depositor), 0.230 (DCC)
R-Value Work: 0.187 (Depositor), 0.200 (DCC)
R-Value Observed: 0.189 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34FVS

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.86	α = 90
b = 154.51	β = 90
c = 72.64	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SOLVE	phasing
SCALA	data scaling
BUSTER-TNT	refinement
MOSFLM	data reduction
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-07-25

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2012-07-25
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-10-30
Changes: Data collection, 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 R01GM157729.