[English] 日本語
Yorodumi
- PDB-6vtp: Crystal structure of G16C human Galectin-7 mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vtp
TitleCrystal structure of G16C human Galectin-7 mutant
ComponentsGalectin-7
KeywordsSUGAR BINDING PROTEIN / Human Galectin-7 / G16C mutant / disulfide bond
Function / homology
Function and homology information


Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / 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
Natural Sciences and Engineering Research Council (NSERC, 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 ...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

-
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)30,2084
Polymers30,0242
Non-polymers1842
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-1 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.600, 67.150, 71.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 19 or resid 22 through 29 or resid 31 through 135))
21(chain B and (resid 4 through 19 or resid 22 through 29 or resid 31 through 135))

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
11PROPROLEULEU(chain A and (resid 4 through 19 or resid 22 through 29 or resid 31 through 135))AA4 - 194 - 19
12ARGARGALAALA(chain A and (resid 4 through 19 or resid 22 through 29 or resid 31 through 135))AA22 - 2922 - 29
13ARGARGPHEPHE(chain A and (resid 4 through 19 or resid 22 through 29 or resid 31 through 135))AA31 - 13531 - 135
21PROPROLEULEU(chain B and (resid 4 through 19 or resid 22 through 29 or resid 31 through 135))BB4 - 194 - 19
22ARGARGALAALA(chain B and (resid 4 through 19 or resid 22 through 29 or resid 31 through 135))BB22 - 2922 - 29
23ARGARGPHEPHE(chain B and (resid 4 through 19 or resid 22 through 29 or resid 31 through 135))BB31 - 13531 - 135

-
Components

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


Mass: 15011.941 Da / Num. of mol.: 2 / Mutation: G16C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS7, PIG1, LGALS7B / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P47929
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Sodium chloride, 0.1M Tris pH 8, 20 % PEG 3350, 15 % 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: 2.3→49.08 Å / Num. obs: 11900 / % possible obs: 98.97 % / Redundancy: 9.68 % / Biso Wilson estimate: 52.768 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.151 / Rrim(I) all: 0.159 / Net I/σ(I): 14.5 / Num. measured all: 115145
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10.01 % / Rmerge(I) obs: 2.416 / Mean I/σ(I) obs: 1.2 / Num. measured obs: 11553 / Num. unique obs: 1154 / CC1/2: 0.569 / Rrim(I) all: 2.545 / % possible all: 98.13

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å49.08 Å
Translation2.5 Å49.08 Å

-
Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.7.12phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bkz

1bkz


Resolution: 2.3→49.08 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2606 1189 10.01 %
Rwork0.214 10687 -
obs0.2189 11876 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.19 Å2 / Biso mean: 65.2367 Å2 / Biso min: 28.01 Å2
Refinement stepCycle: final / Resolution: 2.3→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 12 44 2155
Biso mean--48.07 49.48 -
Num. residues----267
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1194X-RAY DIFFRACTION11.301TORSIONAL
12B1194X-RAY DIFFRACTION11.301TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.40.34551420.37251292143498
2.4-2.530.3281460.33751290143698
2.53-2.690.33911410.28871325146698
2.69-2.90.31451470.27931311145899
2.9-3.190.30641510.23521332148399
3.19-3.650.24611540.20691328148299
3.65-4.60.21961480.17081363151199
4.6-49.080.23881600.1781446160699
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)
13.3551-1.87370.80576.2709-2.05225.99810.362-0.24720.27670.6138-0.39190.5052-0.37681.31090.15380.4893-0.15480.02860.4534-0.07850.5904-0.459-2.087-0.326
23.7026-1.14650.70092.2171-0.21692.1345-0.1470.29250.21120.3738-0.2607-0.4002-0.34020.08060.32240.26290.0087-0.00410.34260.02390.334-3.031-11.447-4.872
34.6882-1.3357-0.55272.2458-0.87522.61950.0942-0.31150.73170.04370.2272-0.0398-0.196-0.0808-0.26440.3341-0.04350.05910.332-0.02830.3916-12.584-10.418-2.51
43.7205-1.12060.04660.9434-0.37792.58030.08040.06910.1140.0039-0.024-0.0390.0012-0.3935-0.02520.3797-0.0254-0.00180.42380.03670.4295-11.997-15.288-5.342
54.9166-1.5919-0.64534.41130.47310.54460.08361.65140.8275-1.0163-0.3038-0.0671-0.1468-0.27730.31120.5362-0.0820.05210.63970.19110.5235-6.447-7.951-16.218
62.1029-0.86670.64867.4822-0.2229.4665-0.63581.05210.051-0.45460.02820.43240.43-0.33370.70260.4161-0.0557-0.00280.35710.02850.3551-4.072-18.535-14.943
73.531-0.5027-2.2035.3627-0.79982.10780.03721.11190.6291-1.01020.32070.4577-0.314-0.627-0.08950.5258-0.0837-0.03860.55580.2140.5045-14.198-6.237-14.522
82.90320.4490.43812.3653-1.72992.49730.01330.22270.52690.2864-0.0983-0.3771-0.35090.22840.11760.3672-0.0012-0.00140.40150.090.4018-1.609-6.37-3.321
92.74260.7315-0.11023.9232-2.86922.37440.645-0.548-0.1875-0.6264-0.4306-1.36740.6663-1.1327-0.05861.123-0.07350.2270.72320.06991.205511.04-20.414-32.025
107.74541.15452.9181.2156-1.45485.4384-1.69930.7646-1.7326-1.34741.37132.40210.4049-1.31590.49220.9838-0.2871-0.05330.97830.14480.8672-2.085-12.045-31.699
117.73290.65182.8151.66722.77085.01961.0864-0.5768-0.7462-0.50860.20210.4334-0.230.73180.27790.5892-0.21610.1640.86720.29640.61234.227-12.62-20.828
121.1221-0.09710.14250.006-0.01390.0165-0.010.1035-0.3917-1.1449-0.4852-1.20930.75720.75580.10370.81240.35170.46160.89260.5421.170819.153-19.374-18.485
130.7018-1.2984-0.85493.64451.33861.0702-0.33720.36-0.9693-1.1506-0.1404-1.27011.14440.52150.22120.87710.0740.45580.78240.22540.950616.993-12.459-29.753
143.3897-0.25621.01455.5871-0.15774.10010.14511.2888-0.4721-1.1151-0.2361-1.6510.86761.81680.07930.860.10550.36980.83760.13970.849217.212-7.59-30.75
152.836-0.3962-1.72295.56921.99814.66050.31090.90010.2922-1.6850.51051.3590.40040.2324-0.22481.5161-0.17630.38330.6563-0.06040.713312.856-2.084-40.838
162.38240.318-0.63112.3746-0.33881.254-0.5483-0.4685-0.3391-0.2681-0.1804-1.39050.19760.95810.20150.63850.1420.15560.83140.19670.796719.494-7.27-21.831
173.83220.8541-0.83233.82240.58783.2194-0.1765-0.44210.28630.3497-0.0178-0.054-0.45620.44430.02740.41980.02630.05150.4380.1190.36076.541-4.345-20.002
183.47450.56531.75223.2070.46064.4973-0.84570.45830.6906-0.36320.65460.269-0.30610.2289-0.04860.67760.0579-0.01050.57720.17830.5257.734-0.245-27.788
199.1212-6.75261.9335.2517-2.55485.48370.26330.4627-0.3192-0.6016-1.45820.30110.7630.99931.01521.2938-0.0280.23570.52770.08340.92817.42-13.55-33.185
206.2126-0.1443-1.02013.1752-0.30912.54560.29620.073-0.2853-0.6016-0.387-1.07951.02310.6440.22670.8984-0.01880.22320.64560.03610.633310.61-19.178-22.839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:12 )A1 - 12
2X-RAY DIFFRACTION2( CHAIN A AND RESID 13:37 )A13 - 37
3X-RAY DIFFRACTION3( CHAIN A AND RESID 38:62 )A38 - 62
4X-RAY DIFFRACTION4( CHAIN A AND RESID 63:87 )A63 - 87
5X-RAY DIFFRACTION5( CHAIN A AND RESID 88:98 )A88 - 98
6X-RAY DIFFRACTION6( CHAIN A AND RESID 99:106 )A99 - 106
7X-RAY DIFFRACTION7( CHAIN A AND RESID 107:115 )A107 - 115
8X-RAY DIFFRACTION8( CHAIN A AND RESID 116:135 )A116 - 135
9X-RAY DIFFRACTION9( CHAIN B AND RESID 4:6 )B4 - 6
10X-RAY DIFFRACTION10( CHAIN B AND RESID 7:15 )B7 - 15
11X-RAY DIFFRACTION11( CHAIN B AND RESID 16:21 )B16 - 21
12X-RAY DIFFRACTION12( CHAIN B AND RESID 22:27 )B22 - 27
13X-RAY DIFFRACTION13( CHAIN B AND RESID 28:39 )B28 - 39
14X-RAY DIFFRACTION14( CHAIN B AND RESID 40:62 )B40 - 62
15X-RAY DIFFRACTION15( CHAIN B AND RESID 63:68 )B63 - 68
16X-RAY DIFFRACTION16( CHAIN B AND RESID 69:88 )B69 - 88
17X-RAY DIFFRACTION17( CHAIN B AND RESID 89:104 )B89 - 104
18X-RAY DIFFRACTION18( CHAIN B AND RESID 105:117 )B105 - 117
19X-RAY DIFFRACTION19( CHAIN B AND RESID 118:124 )B118 - 124
20X-RAY DIFFRACTION20( 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