4N42 | pdb_00004n42

Crystal structure of allergen protein scam1 from Scadoxus multiflorus

PDB DOI: https://doi.org/10.2210/pdb4N42/pdb

Classification: HYDROLASE INHIBITOR
Organism(s): Scadoxus multiflorus
Mutation(s): No

Deposited: 2013-10-08 Released: 2013-10-30
Deposition Author(s): Singh, A., Kumar, S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.196 (Depositor), 0.197 (DCC)
R-Value Work:
0.153 (Depositor), 0.152 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of allergen protein scam1 from Scadoxus multiflorus

Singh, A., Kumar, S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 29.72 kDa
Atom Count: 2,253
Modeled Residue Count: 272
Deposited Residue Count: 272
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylanase and alpha-amylase inhibitor protein isoform III	A	272	Scadoxus multiflorus	Mutation(s): 0 EC: 3.2.1.14
UniProt
Find proteins for E3VTL0 (Scadoxus multiflorus) Explore E3VTL0 Go to UniProtKB: E3VTL0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E3VTL0
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] mmCIF 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.196 (Depositor), 0.197 (DCC)
R-Value Work: 0.153 (Depositor), 0.152 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.736	α = 90
b = 65.265	β = 102.26
c = 49.32	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-10-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-30
Type: Initial release
Version 1.1: 2015-02-11
Changes: Experimental preparation
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-20
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.