4XTP | pdb_00004xtp

Crystal structure of a recombinant Vatairea macrocarpa seed lectin complexed with Tn antigen

PDB DOI: https://doi.org/10.2210/pdb4XTP/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Vatairea macrocarpa
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2015-01-23 Released: 2016-01-27
Deposition Author(s): Sousa, B.L., Silva-Filho, J.C., Kumar, P., Lyskowski, A., Bezerra, G.A., Delatorre, P., Rocha, B.A.M., Cunha, R.M.S., Nagano, C.S., Gruber, K., Cavada, B.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.254 (Depositor), 0.200 (DCC)
R-Value Work:
0.198 (Depositor), 0.210 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of a recombinant Vatairea macrocarpa seed lectin

Sousa, B.L., Silva-Filho, J.C., Kumar, P., Lyskowski, A., Bezerra, G.A., Delatorre, P., Rocha, B.A.M., Cunha, R.M.S., Nagano, C.S., Gruber, K., Cavada, B.S.

(2016) Int J Biochem Cell Biol

Macromolecule Content

Total Structure Weight: 28.78 kDa
Atom Count: 2,035
Modelled Residue Count: 234
Deposited Residue Count: 250
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Seed lectin	A	250	Vatairea macrocarpa	Mutation(s): 0
UniProt
Find proteins for P81371 (Vatairea macrocarpa) Explore P81371 Go to UniProtKB: P81371
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P81371
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A2G Query on A2G Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	2-acetamido-2-deoxy-alpha-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-CBQIKETKSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SER Query on SER Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.254 (Depositor), 0.200 (DCC)
R-Value Work: 0.198 (Depositor), 0.210 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.093	α = 90
b = 86.024	β = 90
c = 128.877	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building
iMOSFLM	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-01-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-01-27
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary