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- PDB-5mwt: Galectin-1 in Complex with Ligand JB97 -

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Basic information

Entry
Database: PDB / ID: 5mwt
TitleGalectin-1 in Complex with Ligand JB97
ComponentsGalectin-1
KeywordsTRANSFERASE / Sucrose Phosphorylase / bisp / Bifidobacterium
Function / homology
Function and homology information


galectin complex / plasma cell differentiation / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / carbohydrate binding ...galectin complex / plasma cell differentiation / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / carbohydrate binding / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / positive regulation of viral entry into host cell / positive regulation of apoptotic process / endoplasmic reticulum lumen / apoptotic process / extracellular space / RNA binding / extracellular exosome / extracellular region / cytosol / cytoplasm
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Chem-JB9 / Galectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.711 Å
AuthorsGrimm, C. / Bechold, J.
CitationJournal: To Be Published
Title: Structural insights into the redesign of a sucrose phosphorylase by induced loop repositioning
Authors: Grimm, C. / Bechold, J.
History
DepositionJan 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-1
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0716
Polymers29,5142
Non-polymers1,5584
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-10 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.290, 58.250, 111.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Galectin-1 / / Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L- ...Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / HBL / HPL / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / Putative MAPK-activating protein PM12 / S-Lac lectin 1


Mass: 14756.753 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09382
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-JB9 / ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-5-[(2~{S},3~{R},4~{S},5~{S},6~{R})-4-[[1-[[3-[(~{Z})-3-[bis(azanyl)methylideneamino]prop-1-enyl]phenyl]methyl]-1,2,3-triazol-4-yl]methoxy]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-6-(hydroxymethyl)-4-oxidanyl-2-prop-2-enoxy-oxan-3-yl]ethanamide / JB97


Mass: 691.729 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H45N7O11
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.5 M AMMONIUM SULFATE, PH 7.5,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.711→60 Å / Num. obs: 30672 / % possible obs: 98 % / Redundancy: 3.9 % / Net I/σ(I): 9.9

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Processing

Software
NameVersionClassification
PHENIXdev_2443refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.711→51.603 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.84
RfactorNum. reflection% reflection
Rfree0.2322 1493 4.87 %
Rwork0.2047 --
obs0.206 30671 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.64 Å2 / Biso mean: 34.5841 Å2 / Biso min: 16.57 Å2
Refinement stepCycle: final / Resolution: 1.711→51.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 111 184 2358
Biso mean--69.55 39.72 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062340
X-RAY DIFFRACTIONf_angle_d0.7393184
X-RAY DIFFRACTIONf_chiral_restr0.052348
X-RAY DIFFRACTIONf_plane_restr0.004420
X-RAY DIFFRACTIONf_dihedral_angle_d15.291465
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7107-1.76590.37641520.3532560271298
1.7659-1.8290.31221430.33752591273498
1.829-1.90220.32211240.31822647277199
1.9022-1.98880.27351330.27692616274999
1.9888-2.09370.30911260.22152645277199
2.0937-2.22490.23181360.20892640277699
2.2249-2.39660.21571190.19972643276299
2.3966-2.63780.20881290.201926932822100
2.6378-3.01950.21791600.20262669282999
3.0195-3.8040.22761280.17092689281797
3.804-51.62670.19331430.16922785292897
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.41264.96572.99455.9979-0.08337.0220.2579-0.1637-0.2244-0.024-0.104-0.00030.66360.1814-0.0850.27890.04260.00720.1619-0.05520.249413.608111.442917.6515
22.1313-4.22426.03275.8521-1.49118.26110.35680.0917-0.4628-0.6478-0.18920.39570.1591-0.0655-0.17760.2588-0.0483-0.02480.19180.03480.25875.674518.45143.5793
31.12470.20520.24262.923-0.87125.10540.00420.01660.1340.06830.0960.1818-0.4138-0.2065-0.08270.2361-0.0130.04550.1814-0.00530.20335.695526.236215.6873
45.0802-0.33912.10894.17770.4273.51680.1641-0.0314-0.0617-0.1589-0.0676-0.17340.06240.1778-0.06280.2198-0.06560.0390.19940.00920.210215.145723.02449.0252
50.281-0.3991-1.86531.06144.79512.01360.1217-0.0093-0.0253-0.0844-0.02260.0141-1.04960.0651-0.11140.3516-0.07310.03510.2799-0.00860.222216.652428.30019.1258
62.3036-1.315-1.40865.9527-1.24811.8958-0.1951-0.089-0.09590.68850.2345-0.346-0.13580.3813-0.08930.2704-0.0103-0.00920.2188-0.01280.177111.984417.752921.1952
72.0388-7.16092.8049.71-2.41017.3991-0.0080.4081-0.08310.04010.10950.42050.13910.3220.06050.2922-0.0307-0.01430.1872-0.00050.298411.05412.07066.8397
85.65272.15822.48414.48854.75378.16040.18450.04250.24880.1965-0.1097-0.1095-0.085-0.0576-0.09770.2295-0.0292-0.01980.13440.0310.21394.60812.866810.8967
94.22540.5679-1.04443.8543-0.96742.4026-0.0106-0.26850.04080.3053-0.0061-0.37440.01560.21790.00430.20770.0047-0.03680.1809-0.03660.16513.1964-5.53614.7666
109.19351.2359-2.51162.02470.92098.01780.2337-0.9867-0.06291.10180.0951-0.75390.54430.1234-0.24020.36250.047-0.08270.33160.03150.314321.8313-16.753618.7783
119.6644-1.7148-5.41622.10470.99163.5261-0.2518-0.2305-0.39110.25990.02660.12310.34330.12490.2140.27570.00340.01550.19680.00580.19288.4082-15.780715.8046
124.59321.79982.34444.9936-0.75344.1439-0.43290.12430.7707-0.09010.0276-1.2096-0.05210.340.37690.21150.0388-0.0220.2492-0.03850.38521.3244-6.66387.4622
138.9495-0.23941.84669.32350.3275.9637-0.07030.3943-0.1142-0.56670.08570.25440.2666-0.285-0.03760.2291-0.014-0.00430.1927-0.00320.15334.1237-9.24422.9747
142.8306-0.2986-1.5692.5171-0.01472.1107-0.07920.2179-0.1407-0.11630.04180.08850.1893-0.15790.01320.1747-0.024-0.02490.1496-0.00820.1085.4099-9.8546.7206
159.5515-0.37930.4946.9146-2.8423.52070.1416-0.09610.12160.10450.0223-0.26810.25950.2974-0.11360.2220.0014-0.01290.1469-0.07520.17414.30741.692211.9497
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 15 )A2 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 29 )A17 - 29
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 76 )A30 - 76
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 99 )A77 - 99
5X-RAY DIFFRACTION5chain 'A' and (resid 100 through 109 )A100 - 109
6X-RAY DIFFRACTION6chain 'A' and (resid 110 through 124 )A110 - 124
7X-RAY DIFFRACTION7chain 'A' and (resid 125 through 134 )A125 - 134
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 15 )B2 - 15
9X-RAY DIFFRACTION9chain 'B' and (resid 17 through 48 )B17 - 48
10X-RAY DIFFRACTION10chain 'B' and (resid 49 through 56 )B49 - 56
11X-RAY DIFFRACTION11chain 'B' and (resid 57 through 76 )B57 - 76
12X-RAY DIFFRACTION12chain 'B' and (resid 77 through 89 )B77 - 89
13X-RAY DIFFRACTION13chain 'B' and (resid 90 through 99 )B90 - 99
14X-RAY DIFFRACTION14chain 'B' and (resid 100 through 118 )B100 - 118
15X-RAY DIFFRACTION15chain 'B' and (resid 119 through 134 )B119 - 134

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