4LBQ | pdb_00004lbq

Crystal structure of mouse galectin-1

PDB DOI: https://doi.org/10.2210/pdb4LBQ/pdb

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

Deposited: 2013-06-20 Released: 2014-07-02
Deposition Author(s): Rustiguel, J.K., Trabuco, A.C., Del Cistia Andrade, C., Stowell, S.R., Cummings, R.D., Dias-Baruffi, M., Nonato, M.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.186 (Depositor), 0.187 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of mouse galectin-1

Rustiguel, J.K., Trabuco, A.C., Del Cistia Andrade, C., Stowell, S.R., Cummings, R.D., Dias-Baruffi, M., Nonato, M.C.

To be published.

Macromolecule Content

Total Structure Weight: 59.95 kDa
Atom Count: 4,258
Modeled Residue Count: 521
Deposited Residue Count: 540
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-1	A	135	Mus musculus	Mutation(s): 0 Gene Names: Gbp, Lgals1
UniProt
Find proteins for P16045 (Mus musculus) Explore P16045 Go to UniProtKB: P16045
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16045
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-1	B, C	135	Mus musculus	Mutation(s): 0 Gene Names: Gbp, Lgals1
UniProt
Find proteins for P16045 (Mus musculus) Explore P16045 Go to UniProtKB: P16045
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16045
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-1	D	135	Mus musculus	Mutation(s): 0 Gene Names: Gbp, Lgals1
UniProt
Find proteins for P16045 (Mus musculus) Explore P16045 Go to UniProtKB: P16045
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16045
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.186 (Depositor), 0.187 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.04	α = 90
b = 38.2	β = 112.71
c = 130.18	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-07-02

Deposition Author(s):

Rustiguel, J.K.

Trabuco, A.C.

Del Cistia Andrade, C.

Revision History (Full details and data files)

Version 1.0: 2014-07-02
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-12-06
Changes: Data collection
Version 1.4: 2024-11-20
Changes: Structure summary