3EHK | pdb_00003ehk

Crystal structure of Pru du amandin, an allergenic protein from prunus dulcis

PDB DOI: https://doi.org/10.2210/pdb3EHK/pdb

Classification: PLANT PROTEIN
Organism(s): Prunus dulcis
Mutation(s): No

Deposited: 2008-09-13 Released: 2009-09-15
Deposition Author(s): Gaur, V., Salunke, D.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.279 (Depositor), 0.277 (DCC)
R-Value Work:
0.254 (Depositor), 0.254 (DCC)
R-Value Observed:
0.257 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Pru du amandin, an allergenic protein from prunus dulcis

Gaur, V., Salunke, D.M.

To be published.

Macromolecule Content

Total Structure Weight: 365.63 kDa
Atom Count: 18,359
Modeled Residue Count: 2,304
Deposited Residue Count: 3,186
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prunin	A, B, C, D, E A, B, C, D, E, F	531	Prunus dulcis	Mutation(s): 0
UniProt
Find proteins for Q43607 (Prunus dulcis) Explore Q43607 Go to UniProtKB: Q43607
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q43607
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.279 (Depositor), 0.277 (DCC)
R-Value Work: 0.254 (Depositor), 0.254 (DCC)
R-Value Observed: 0.257 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.099	α = 90
b = 151.099	β = 90
c = 164.628	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-09-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-09-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-16
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.