6VJ0 | pdb_00006vj0

Crystal structure of a chitin-binding protein from Moringa oleifera seeds (Mo-CBP4)

PDB DOI: https://doi.org/10.2210/pdb6VJ0/pdb

Classification: PLANT PROTEIN
Organism(s): Moringa oleifera
Mutation(s): No

Deposited: 2020-01-14 Released: 2021-01-27
Deposition Author(s): Bezerra, E.H.S., Lopes, T.D.P., da Silva, F.M.S., Costa, H.P.S., Freire, V.N., Rocha, B.A.M., Sousa, D.O.B.
Funding Organization(s): Coordination for the Improvement of Higher Education Personnel

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.227 (Depositor), 0.229 (DCC)
R-Value Work:
0.198 (Depositor), 0.203 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural characterization of a lectin from Moringa oleifera seeds with imflammatory activities

Lopes, T.D.P., Costa, H.P.S., Pereira, M.L., Neto, J.X.S., de Alencar, N.M.N., Vasconcelos, I.M., Oliveira, J.T.A., da Silva, F.M.S., Freire, V.N., Bezerra, E.H.S., Rocha, B.A.M., Sousa, D.O.B.

To be published.

Macromolecule Content

Total Structure Weight: 14.48 kDa
Atom Count: 804
Modeled Residue Count: 90
Deposited Residue Count: 124
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitin-binding protein Mo-CBP4	A	124	Moringa oleifera	Mutation(s): 0
UniProt
Find proteins for W5S2D2 (Moringa oleifera) Explore W5S2D2 Go to UniProtKB: W5S2D2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W5S2D2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.227 (Depositor), 0.229 (DCC)
R-Value Work: 0.198 (Depositor), 0.203 (DCC)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.052	α = 90
b = 107.052	β = 90
c = 42.958	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-01-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Coordination for the Improvement of Higher Education Personnel	Brazil	--

Revision History (Full details and data files)

Version 1.0: 2021-01-27
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary

6VJ0 | pdb_00006vj0

Crystal structure of a chitin-binding protein from Moringa oleifera seeds (Mo-CBP4)

Literature

Structural characterization of a lectin from Moringa oleifera seeds with imflammatory activities

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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