4IZX | pdb_00004izx

Macrolepiota procera ricin B-like lectin (MPL) in complex with lactose

PDB DOI: https://doi.org/10.2210/pdb4IZX/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Macrolepiota procera
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-01-30 Released: 2013-11-20
Deposition Author(s): Renko, M., Zurga, S., Sabotic, J., Pohleven, J., Kos, J., Turk, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.132 (Depositor), 0.150 (DCC)
R-Value Work:
0.107 (Depositor)
R-Value Observed:
0.109 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 3.1 of the entry. See complete history.

Literature

Macrolepiota procera ricin B-like lectin (MPL) in complex with lactose

Renko, M., Zurga, S., Sabotic, J., Pohleven, J., Kos, J., Turk, D.

To be published.

Macromolecule Content

Total Structure Weight: 16.26 kDa
Atom Count: 1,394
Modeled Residue Count: 139
Deposited Residue Count: 140
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin B-like lectin	A	140	Macrolepiota procera	Mutation(s): 0
UniProt
Find proteins for F6KMV5 (Macrolepiota procera) Explore F6KMV5 Go to UniProtKB: F6KMV5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F6KMV5
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G84224TW GlyCosmos: G84224TW GlyGen: G84224TW

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEN Query on BEN 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]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004 Query on PRD_900004	B	beta-lactose	Oligosaccharide / Nutrient		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.132 (Depositor), 0.150 (DCC)
R-Value Work: 0.107 (Depositor)
R-Value Observed: 0.109 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.8	α = 90
b = 57.158	β = 90
c = 61.229	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
PHASER	phasing
MAIN	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-11-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-11-20
Type: Initial release
Version 1.1: 2017-11-15
Changes: Advisory, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 3.0: 2021-08-04
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 3.1: 2023-09-20
Changes: Advisory, Data collection, Database references, Refinement description