4OZD | pdb_00004ozd

Crystal structure of PdSP15a

PDB DOI: https://doi.org/10.2210/pdb4OZD/pdb

Classification: PROTEIN BINDING
Organism(s): Phlebotomus duboscqi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-02-14 Released: 2015-03-04
Deposition Author(s): Andersen, J.F., Alvarenga, P.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.263 (Depositor), 0.264 (DCC)
R-Value Work:
0.200 (Depositor), 0.205 (DCC)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4OZD

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

Literature

Protection against cutaneous leishmaniasis in non-human primates by immunization with an insect salivary protein

Oliveira, F., Rowton, E., Gomes, R., Castrovinci, P.A., Lawyer, P.G., Teixeira, C., Aslan, H., Kleeman, L., Meneses, C., Rowland, T., Gilmore, D., Andersen, J., Alvarenga, P.H., Kamhawi, S., Valenzuela, J.G.

To be published.

Macromolecule Content

Total Structure Weight: 101.27 kDa
Atom Count: 7,008
Modeled Residue Count: 840
Deposited Residue Count: 854
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14.4 kDa salivary protein	A, B, C, D, E A, B, C, D, E, F, G	122	Phlebotomus duboscqi	Mutation(s): 0 Gene Names: M02
UniProt
Find proteins for Q06KA5 (Phlebotomus duboscqi) Explore Q06KA5 Go to UniProtKB: Q06KA5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06KA5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.263 (Depositor), 0.264 (DCC)
R-Value Work: 0.200 (Depositor), 0.205 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.558	α = 90
b = 79.73	β = 90
c = 232.294	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	phasing
PHASER	phasing
PDB_EXTRACT	data extraction
PHENIX	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-03-04

Deposition Author(s):

Alvarenga, P.H.

Revision History (Full details and data files)

Version 1.0: 2015-03-04
Type: Initial release
Version 1.1: 2015-05-20
Changes: Structure summary
Version 1.2: 2017-11-22
Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
Version 1.3: 2018-03-21
Changes: Data collection, Source and taxonomy
Version 1.4: 2023-12-27
Changes: Data collection, Database references, Refinement description
Version 1.5: 2024-10-23
Changes: Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.