4HSD | pdb_00004hsd

Crystal structure of a new form of plant lectin from Cicer arietinum at 2.45 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb4HSD/pdb

Classification: PLANT PROTEIN
Organism(s): Cicer arietinum
Mutation(s): No

Deposited: 2012-10-30 Released: 2012-11-14
Deposition Author(s): Kumar, S., Singh, A., Bhushan, A., Dey, S., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.289 (Depositor), 0.283 (DCC)
R-Value Work:
0.256 (Depositor), 0.255 (DCC)
R-Value Observed:
0.258 (Depositor)

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

Literature

Crystal structure of a new form of plant lectin from Cicer arietinum at 2.45 Angstrom resolution

Kumar, S., Singh, A., Bhushan, A., Dey, S., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 51.5 kDa
Atom Count: 3,816
Modeled Residue Count: 448
Deposited Residue Count: 454
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin	A, B	227	Cicer arietinum	Mutation(s): 0
UniProt
Find proteins for G1K3R9 (Cicer arietinum) Explore G1K3R9 Go to UniProtKB: G1K3R9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1K3R9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-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: 2.45 Å
R-Value Free: 0.289 (Depositor), 0.283 (DCC)
R-Value Work: 0.256 (Depositor), 0.255 (DCC)
R-Value Observed: 0.258 (Depositor)

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.481	α = 90
b = 80.481	β = 90
c = 69.177	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-11-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-11-14
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, 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.