[English] 日本語
Yorodumi
- PDB-6vtr: Crystal structure of G16S human Galectin-7 mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vtr
TitleCrystal structure of G16S human Galectin-7 mutant
ComponentsGalectin-7
KeywordsSUGAR BINDING PROTEIN / Human Galectin-7 / lactose-furanose
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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
Fonds de Recherche du Quebec - Sante (FRQS)Research Scholar Senior Career Award (281993) Canada
Fonds de Recherche du Quebec - Sante (FRQS)Junior 1 (251848) Canada
RGPIN-2017-06091 Canada
Fonds de Recherche du Quebec - Sante (FRQS)Doctoral Training scholarship (287239) Canada
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Perturbing dimer interactions and allosteric communication modulates the immunosuppressive activity of human galectin-7.
Authors: Pham, N.T.H. / Letourneau, M. / Fortier, M. / Begin, G. / Al-Abdul-Wahid, M.S. / Pucci, F. / Folch, B. / Rooman, M. / Chatenet, D. / St-Pierre, Y. / Lague, P. / Calmettes, C. / Doucet, N.
History
DepositionFeb 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 24, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,2064
Polymers29,9922
Non-polymers2142
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.010, 66.700, 71.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 14995.877 Da / Num. of mol.: 2 / Mutation: G16S
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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M NaCl, 0.1 M Tris pH 8.0, 20 % PEG 3350, 17.5 % Glycerol
Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.0332 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 19, 2019 / Details: 16 tiled fiber-optic tapers
RadiationMonochromator: KOHZU double crystal mochochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→48.75 Å / Num. obs: 19128 / % possible obs: 91.2 % / Redundancy: 9.641 % / Biso Wilson estimate: 43.62 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.072 / Χ2: 1.055 / Net I/σ(I): 20.41 / Num. measured all: 184406 / Scaling rejects: 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-2.018.8442.3770.8616751320618940.422.52559.1
2.01-2.149.3711.3351.7725003298326680.6861.41289.4
2.14-2.2810.0460.6963.7924642250924530.9210.73397.8
2.28-2.459.9840.4166.1222744233322780.9610.43897.6
2.45-2.649.9830.23810.2419197194819230.9880.25198.7
2.64-2.869.8810.15714.7516235167516430.9940.16698.1
2.86-3.139.8190.08725.8814070144514330.9980.09299.2
3.13-3.459.7760.05138.4911546119911810.9990.05498.5
3.45-3.859.6410.03552.36961210049970.9990.03799.3
3.85-4.359.6360.02961.85745878177410.0399.1
4.35-59.4970.02470.54594563162610.02599.2
5-48.758.9050.02271.55112031267125810.02499.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.94 Å48.75 Å
Translation5.94 Å48.75 Å

-
Processing

Software
NameVersionClassificationNB
PHENIXdev_2481refinement
MOSFLMdata reduction
Aimless0.5.27data scaling
PHASER2.7.12phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bkz

1bkz


Resolution: 2.3→48.75 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2558 1164 9.88 %
Rwork0.2031 10616 -
obs0.2084 11780 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.77 Å2 / Biso mean: 60.8482 Å2 / Biso min: 26.76 Å2
Refinement stepCycle: final / Resolution: 2.3→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2093 0 14 55 2162
Biso mean--53.9 47.4 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022184
X-RAY DIFFRACTIONf_angle_d0.5772965
X-RAY DIFFRACTIONf_chiral_restr0.048313
X-RAY DIFFRACTIONf_plane_restr0.004403
X-RAY DIFFRACTIONf_dihedral_angle_d13.031320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.40470.34081350.2913129398
2.4047-2.53150.34591460.2845128998
2.5315-2.69010.35271420.2833130298
2.6901-2.89770.30181420.2605130799
2.8977-3.18930.30471470.2357132499
3.1893-3.65070.25741390.1978132399
3.6507-4.59890.19571530.1663135199
4.5989-48.750.23241600.1692142799
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)
17.853-1.8357-2.03618.9405-2.43173.1668-0.37420.25550.26840.60280.56250.29950.18371.6004-0.21440.726-0.1088-0.05650.5076-0.20610.546226.768-2.93490.7825
24.7808-0.58471.11346.52364.7768.9092-0.27220.30561.2364-0.35540.37760.3833-1.09681.0535-0.22460.69540.03770.12790.45020.13650.570524.80042.2647-14.8596
33.2534-1.78280.65562.8983-0.17430.8007-0.128-0.180.26130.16950.0861-0.3606-0.11440.02240.06710.37760.04240.00810.49070.01010.419523.8961-14.2882-1.5888
46.00983.9891-4.00264.26-1.02094.30190.2349-0.81881.77081.27071.0436-0.44640.01460.5013-1.27670.8230.02210.07630.8341-0.16181.087715.35692.60980.6442
53.2215-0.03210.57951.88610.67873.92990.14580.1829-0.02230.0856-0.19170.00710.0668-0.17170.03680.333-0.0260.00050.37520.02080.396713.9558-15.0324-3.7269
66.2887-2.73880.46611.0828-0.04342.65370.29230.30510.0357-0.2499-0.16490.01080.0781-0.1725-0.1490.3955-0.09080.03640.37770.02270.419115.5663-15.6603-5.4495
76.359-1.6991-0.3116.24170.38112.3017-0.02451.70630.4034-0.2827-0.1210.0532-0.34130.11080.12970.342-0.03050.02110.53290.08910.398621.4046-9.5182-15.481
82.1116-3.7949-1.03439.0996-0.6959.99630.44060.73330.0343-0.4316-1.0657-0.72190.00550.00770.75720.5014-0.05890.06450.51990.02620.43121.5885-18.7631-15.2474
95.1-0.1406-2.46457.917-1.73261.97150.30060.54040.6032-0.8293-0.10360.56950.1042-0.026-0.13920.43670.0534-0.03510.57780.27370.612813.0245-4.3193-14.433
107.5606-3.14052.86236.3471-0.55574.7932-0.43680.30910.22450.08161.49091.1495-0.7905-0.2798-0.94410.4629-0.08940.08130.67160.07780.639219.78761.0005-4.9807
111.2127-1.44021.40573.1011-0.97834.90690.06190.10240.260.09070.00430.1417-0.29320.1787-0.01660.3922-0.0334-0.00960.49770.02260.458829.3286-10.5311-2.0672
122.4901-3.11870.58836.38280.03354.59370.02420.1095-1.0419-1.71570.29680.71241.5943-0.431-0.16591.8375-0.38250.08080.8165-0.01190.944931.6892-17.6637-32.7995
131.0396-0.3438-1.17835.736-1.09565.00350.05520.1364-0.6178-0.56980.46220.87960.3711-1.1512-0.35450.4756-0.174-0.01260.85460.08260.505527.0773-9.5554-24.4357
144.6881-0.1692-0.49991.47450.53920.2089-0.65560.2751-0.2748-2.269-0.7838-1.94772.27711.24870.82811.07030.28650.55140.81660.37051.141844.7721-14.4654-25.8765
152.18381.09240.47792.49432.27116.32170.29720.6193-0.9501-2.1502-0.3577-1.08912.2745-0.00430.05961.6090.03240.30220.78790.0580.690438.9658-9.1464-35.8851
161.0818-0.5895-0.64520.28440.31850.39130.86970.3788-0.2884-0.1411-2.2769-2.87350.38522.17430.63330.6770.21060.10911.34140.58711.493252.1452-6.1825-24.2102
173.79021.2507-2.98293.64272.1647.971-0.3980.6013-0.9902-0.8874-0.22-0.03760.6915-0.39630.4740.9731-0.06690.31770.5966-0.00670.670640.9458-2.0794-36.7401
183.9001-1.1412-0.33723.6325-1.2970.5662-0.6379-0.02470.3383-0.873-0.4662-1.26031.250.24650.80590.64-0.03450.10620.61110.20990.661546.6344-1.4025-26.9561
192.2504-0.07950.10084.6769-0.06074.2982-0.39310.1971-0.02540.08160.0086-0.74890.2510.1440.35220.4799-0.00840.09220.55460.18840.579938.7804-8.3585-19.2117
205.5170.87930.45272.57430.0953.50790.0351-0.09050.188-0.73770.3436-0.08760.6941-0.7086-0.34730.5863-0.11620.05480.48050.12470.357435.1319-1.2427-26.4794
212.1241-0.47732.11426.682-3.85939.02020.08140.68710.2506-2.1257-0.6384-0.6391.31461.70540.73711.7915-0.14740.23060.818-0.05430.713935.4932-14.3337-32.9701
227.0424-0.2402-1.30792.46240.48534.37080.22880.0087-0.4378-0.5662-0.4667-0.79630.63530.4080.11070.72060.01920.17170.64430.06390.584838.0175-19.1349-22.8021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:10)A2 - 10
2X-RAY DIFFRACTION2(chain A and resid 11:17)A11 - 17
3X-RAY DIFFRACTION3(chain A and resid 18:37)A18 - 37
4X-RAY DIFFRACTION4(chain A and resid 38:45)A38 - 45
5X-RAY DIFFRACTION5(chain A and resid 46:64)A46 - 64
6X-RAY DIFFRACTION6(chain A and resid 65:87)A65 - 87
7X-RAY DIFFRACTION7(chain A and resid 88:101)A88 - 101
8X-RAY DIFFRACTION8(chain A and resid 102:107)A102 - 107
9X-RAY DIFFRACTION9(chain A and resid 108:116)A108 - 116
10X-RAY DIFFRACTION10(chain A and resid 117:122)A117 - 122
11X-RAY DIFFRACTION11(chain A and resid 123:135)A123 - 135
12X-RAY DIFFRACTION12(chain B and resid 4:11)B4 - 11
13X-RAY DIFFRACTION13(chain B and resid 12:20)B12 - 20
14X-RAY DIFFRACTION14(chain B and resid 21:39)B21 - 39
15X-RAY DIFFRACTION15(chain B and resid 40:51)B40 - 51
16X-RAY DIFFRACTION16(chain B and resid 52:60)B52 - 60
17X-RAY DIFFRACTION17(chain B and resid 61:67)B61 - 67
18X-RAY DIFFRACTION18(chain B and resid 68:80)B68 - 80
19X-RAY DIFFRACTION19(chain B and resid 81:102)B81 - 102
20X-RAY DIFFRACTION20(chain B and resid 103:118)B103 - 118
21X-RAY DIFFRACTION21(chain B and resid 119:124)B119 - 124
22X-RAY DIFFRACTION22(chain B and resid 125:135)B125 - 135

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more