7LJG | pdb_00007ljg

Crystal Structure of Lectin from Dioclea altissima

PDB DOI: https://doi.org/10.2210/pdb7LJG/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Macropsychanthus violaceus
Mutation(s): No

Deposited: 2021-01-29 Released: 2022-02-09
Deposition Author(s): Vieira-Neto, A.E., Pereira, H.M., Sousa, F.D., Goncalves, N.G.G., Vieira, N.C.G., Monteiro-Moreira, A.C.O., Moereira, R.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free:
0.249 (Depositor), 0.252 (DCC)
R-Value Work:
0.215 (Depositor), 0.219 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Lectin from Dioclea altissima

Vieira-Neto, A.E., Pereira, H.M., Sousa, F.D., Goncalves, N.G.G., Vieira, N.C.G., Monteiro-Moreira, A.C.O., Moereira, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 51.07 kDa
Atom Count: 3,539
Modeled Residue Count: 450
Deposited Residue Count: 474
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin	A, B	237	Macropsychanthus violaceus	Mutation(s): 0
UniProt
Find proteins for I1SB09 (Dioclea violacea) Explore I1SB09 Go to UniProtKB: I1SB09
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I1SB09
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN 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]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-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: 2.21 Å
R-Value Free: 0.249 (Depositor), 0.252 (DCC)
R-Value Work: 0.215 (Depositor), 0.219 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.958	α = 90
b = 71.958	β = 90
c = 161.906	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2022-02-09

Deposition Author(s):

Vieira-Neto, A.E.

Goncalves, N.G.G.

Monteiro-Moreira, A.C.O.

Revision History (Full details and data files)

Version 1.0: 2022-02-09
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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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.