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- PDB-7rdg: Crystal structure of D103A human Galectin-7 mutant in presence of... -

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Basic information

Entry
Database: PDB / ID: 7rdg
TitleCrystal structure of D103A human Galectin-7 mutant in presence of lactose
ComponentsGalectin-7
KeywordsSUGAR BINDING PROTEIN / human galectin-7 / dimer interface mutant / D103A / lactose
Function / homology
Function and homology information


heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / apoptotic process / extracellular space / extracellular exosome / nucleus / cytoplasm
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
alpha-lactose / Galectin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPham, N.T.H. / Calmettes, C. / Doucet, N.
Funding support Canada, United States, 6items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN 2016-05557 Canada
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM105978 United States
Other governmentFonds de Recherche du Quebec - Sante (FRQ-S) - Research Scholar Senior Career Award (281993) Canada
Other governmentFonds de Recherche du Quebec - Sante (FRQ-S) - Junior 1 (251848) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2017-06091 Canada
Other governmentFonds de Recherche du Quebec - Sante (FRQ-S) - Doctoral Training scholarship (287239) Canada
CitationJournal: To Be Published
Title: Crystal structure of D103A human Galectin-7 mutant in presence of lactose
Authors: Pham, N.T.H. / Calmettes, C. / Doucet, N.
History
DepositionJul 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Galectin-7
B: Galectin-7
A: Galectin-7
D: Galectin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,24311
Polymers59,6874
Non-polymers1,5557
Water1,62190
1
C: Galectin-7
hetero molecules

D: Galectin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5905
Polymers29,8442
Non-polymers7473
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
2
B: Galectin-7
A: Galectin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6526
Polymers29,8442
Non-polymers8094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.330, 112.280, 77.040
Angle α, β, γ (deg.)90.000, 91.080, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 127 or resid 129 through 135 or resid 201))
21(chain B and (resid 3 through 127 or resid 129 through 135 or resid 201))
31(chain C and (resid 3 through 127 or resid 129 through 135 or resid 201))
41(chain D and (resid 3 through 127 or resid 129 through 135 or resid 201))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALVALVAL(chain A and (resid 3 through 127 or resid 129 through 135 or resid 201))AC3 - 1273 - 127
12LEULEUPHEPHE(chain A and (resid 3 through 127 or resid 129 through 135 or resid 201))AC129 - 135129 - 135
13EDOEDOEDOEDO(chain A and (resid 3 through 127 or resid 129 through 135 or resid 201))AJ201
21VALVALVALVAL(chain B and (resid 3 through 127 or resid 129 through 135 or resid 201))BB3 - 1273 - 127
22LEULEUPHEPHE(chain B and (resid 3 through 127 or resid 129 through 135 or resid 201))BB129 - 135129 - 135
23HOHHOHHOHHOH(chain B and (resid 3 through 127 or resid 129 through 135 or resid 201))BM201
31VALVALVALVAL(chain C and (resid 3 through 127 or resid 129 through 135 or resid 201))CA3 - 1273 - 127
32LEULEUPHEPHE(chain C and (resid 3 through 127 or resid 129 through 135 or resid 201))CA129 - 135129 - 135
33EDOEDOEDOEDO(chain C and (resid 3 through 127 or resid 129 through 135 or resid 201))CI201
41VALVALVALVAL(chain D and (resid 3 through 127 or resid 129 through 135 or resid 201))DD3 - 1273 - 127
42LEULEUPHEPHE(chain D and (resid 3 through 127 or resid 129 through 135 or resid 201))DD129 - 135129 - 135
43HOHHOHHOHHOH(chain D and (resid 3 through 127 or resid 129 through 135 or resid 201))DO201

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Components

#1: Protein
Galectin-7 / Gal-7 / HKL-14 / PI7 / p53-induced gene 1 protein


Mass: 14921.840 Da / Num. of mol.: 4 / Mutation: D103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS7, PIG1, LGALS7B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P47929
#2: Polysaccharide
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.1 M Tris pH 7.3, 0.1 M NaCl, 18% P400, 26% PEG 3350
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.5214 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5214 Å / Relative weight: 1
ReflectionResolution: 3→38.51 Å / Num. obs: 10243 / % possible obs: 100 % / Redundancy: 3.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.047 / Rrim(I) all: 0.086 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3-3.113.20.1587.310230.9780.1050.19198.2
3.11-3.233.10.1328.410020.9810.090.16198.3
3.23-3.383.30.1110.110450.9850.0720.13299
3.38-3.563.10.09311.19840.9850.0640.11497.9
3.56-3.783.30.08212.810410.9880.0640.09898.1
3.78-4.073.20.07613.39870.9870.050.09198.8
4.07-4.483.20.06215.410410.9940.040.07498.5
4.48-5.133.30.05316.410460.9950.0340.06399.7
5.13-6.453.30.0616.110210.9910.0390.07299.1
6.45-36.433.30.05316.910530.9950.0350.06399.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bkz

4bkz


Resolution: 3→38.51 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2684 873 8.53 %
Rwork0.2041 9359 -
obs0.2096 10232 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 197.98 Å2 / Biso mean: 35.8077 Å2 / Biso min: 11.28 Å2
Refinement stepCycle: final / Resolution: 3→38.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4172 0 210 92 4474
Biso mean--35.42 33.67 -
Num. residues----533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154388
X-RAY DIFFRACTIONf_angle_d1.6995952
X-RAY DIFFRACTIONf_dihedral_angle_d15.6661607
X-RAY DIFFRACTIONf_chiral_restr0.086654
X-RAY DIFFRACTIONf_plane_restr0.012792
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2499X-RAY DIFFRACTION15.142TORSIONAL
12B2499X-RAY DIFFRACTION15.142TORSIONAL
13C2499X-RAY DIFFRACTION15.142TORSIONAL
14D2499X-RAY DIFFRACTION15.142TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.190.35071350.28361546168198
3.19-3.430.32321470.24191570171799
3.43-3.780.26371480.20531544169298
3.78-4.320.29031440.18081552169699
4.33-5.450.19251440.16061557170199
5.45-38.510.27091550.21241590174599

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