3K2D

Crystal structure of Immunogenic lipoprotein A from Vibrio vulnificus

PDB DOI: https://doi.org/10.2210/pdb3K2D/pdb

Classification: IMMUNE SYSTEM
Organism(s): Vibrio vulnificus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-09-30 Released: 2010-10-13
Deposition Author(s): Yu, S., Rhee, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.263
R-Value Work: 0.225

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Toll-like receptor 2-activating lipoprotein IIpA from Vibrio vulnificus.

Yu, S., Lee, N.Y., Park, S.J., Rhee, S.

(2011) Proteins 79: 1020-1025

PubMed: 21287630 Search on PubMed
DOI: https://doi.org/10.1002/prot.22929
Primary Citation of Related Structures:
3K2D

Organizational Affiliation

Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.

Macromolecule Content

Total Structure Weight: 52.39 kDa
Atom Count: 3,776
Modelled Residue Count: 467
Deposited Residue Count: 474
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC-type metal ion transport system, periplasmic component	A, B	237	Vibrio vulnificus	Mutation(s): 4 Gene Names: VV1_0294
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MET Query on MET Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	METHIONINE C₅ H₁₁ N O₂ S FFEARJCKVFRZRR-BYPYZUCNSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.263
R-Value Work: 0.225
Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 273.6	α = 90
b = 273.6	β = 90
c = 273.6	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-10-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-04-18
Changes: Database references
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2021-11-10
Changes: Database references, Derived calculations
Version 1.5: 2024-05-29
Changes: Data collection

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.