[English] 日本語
Yorodumi
- PDB-7n6c: Crystal structure of R22A human Galectin-7 mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n6c
TitleCrystal structure of R22A human Galectin-7 mutant
ComponentsGalectin-7
KeywordsSUGAR BINDING PROTEIN / human Galectin-7 / dimer interface mutant
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
DI(HYDROXYETHYL)ETHER / Galectin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 R20A human Galectin-7 mutant
Authors: Pham, N.T.H. / Calmettes, C. / Doucet, N.
History
DepositionJun 8, 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 / 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)30,57412
Polymers29,7592
Non-polymers81510
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.350, 64.890, 71.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 14879.734 Da / Num. of mol.: 2 / Mutation: R22A
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

-
Non-polymers , 5 types, 127 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: 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 / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M NaCl, 0.1 M Tris pH 8, 20 % PEG 6000, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.05→48.19 Å / Num. obs: 16194 / % possible obs: 99.9 % / Redundancy: 10.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.127 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible allRpim(I) all
2.05-2.1210.21.3711.815700.6851.44399.8
2.12-2.2110.20.982.515870.7871.03199.90.318
2.21-2.3110.20.6773.715970.8980.71399.90.22
2.31-2.4310.20.5244.715930.9280.552100
2.43-2.5810.20.4026.216000.9590.4231000.13
2.58-2.7810.20.2858.516080.9790.31000.093
2.78-3.06130.1731316090.9920.18299.90.057
3.06-3.51100.120.516360.9970.1061000.033
3.51-4.429.90.06529.716540.9980.0681000.021
4.42-48.199.40.0534.317400.9980.05299.80.017

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.9 Å48.17 Å
Translation5.9 Å48.17 Å

-
Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XSCALEdata scaling
PHASER2.7.12phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bkz

1bkz


Resolution: 2.1→48.17 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 1510 10 %
Rwork0.1972 13591 -
obs0.201 15101 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.77 Å2 / Biso mean: 48.8005 Å2 / Biso min: 15.65 Å2
Refinement stepCycle: final / Resolution: 2.1→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 129 117 2344
Biso mean--69.01 42.69 -
Num. residues----269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.170.27021360.24412111347
2.17-2.250.33431340.24812101344
2.25-2.340.30181340.248312111345
2.34-2.440.29521350.232812151350
2.44-2.570.29541370.234112231360
2.57-2.730.27281340.223812121346
2.73-2.940.26381360.226312261362
2.94-3.240.27631370.20712391376
3.24-3.710.2161390.174812451384
3.71-4.670.17251410.150512721413
4.67-48.170.20991470.19513271474
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)
10.5777-0.05150.37640.0048-0.01332.06410.09230.07580.210.24730.44051.294-0.5463-0.9445-0.43690.64010.0464-0.14340.45560.33351.3416-1.2372-24.49124.9502
23.5225-1.5441-2.34117.03444.17283.1615-0.00230.0078-0.53530.3583-0.10270.67390.3982-0.08530.09190.3833-0.0461-0.10630.26910.0320.47521.063-33.2844-8.51
33.8002-1.1769-2.70942.83383.5999.1142-0.1380.3147-0.57340.3267-0.10670.26640.6269-0.41160.27440.279-0.0590.00610.29780.02170.2738-0.1633-25.1644-15.1494
41.4747-0.4128-0.33811.76830.45461.1275-0.0845-0.00060.07370.04370.203-0.16170.13280.0423-0.09110.2145-0.0175-0.02220.25870.02720.24229.8388-20.4464-2.3494
53.811-0.9141-0.39811.4597-0.67691.50880.0920.1287-0.1853-0.1424-0.01040.2181-0.14460.0639-0.07760.1975-0.0543-0.03410.24530.02410.300510.9402-15.5482-5.5201
62.5698-1.1337-0.46673.26740.78962.50550.00650.3940.1986-0.44540.0965-0.02660.00330.0908-0.08540.24-0.054-0.00740.3470.03790.19877.7782-19.2609-16.5849
70.72630.32-0.24622.420.93471.7377-0.10460.0559-0.1915-0.05720.01380.13320.301-0.05980.08920.2354-0.02530.00810.24360.03620.27261.7934-26.7036-6.0802
82.8452-0.6704-1.11395.6596-0.01634.81180.20410.26070.4416-0.1027-0.188-0.0801-0.1569-0.6688-0.06310.4860.1147-0.07420.53250.00060.4158-7.2117-11.0289-32.271
94.4963-2.4373-2.10865.04063.89683.3950.3953-0.27080.5428-0.66250.4827-0.3863-0.15641.2129-0.80670.4283-0.03940.03320.3684-0.05630.2723-1.4829-18.9637-23.9375
103.0237-0.347-0.36591.55190.26893.07220.28830.29920.2328-0.4174-0.02570.34660.0026-0.6296-0.18740.43850.012-0.11550.35680.01210.4487-16.5062-16.6874-31.0043
114.1183-1.8638-0.5282.90550.88464.44410.07010.3125-0.6769-0.37820.22720.57460.7705-1.3793-0.33210.5747-0.1789-0.18560.5330.08690.6363-21.1818-24.7707-30.2569
123.82053.0656-2.29476.1076-4.84123.8516-0.01030.0472-0.9674-0.4179-0.2288-0.38320.76990.42040.33820.99270.0519-0.20460.485-0.14870.7365-15.859-27.911-40.9047
132.0484-1.3847-0.01923.5331.71953.58270.2196-0.8275-0.8882-0.30490.14590.9732-0.2203-0.7234-0.4230.5033-0.0994-0.08020.58670.22590.6475-21.2158-21.7272-20.5881
144.2323-0.57080.02292.81750.07753.07630.0784-0.1883-0.809-0.2085-0.16240.48970.8048-0.10690.08830.4697-0.026-0.06290.276-0.00740.3842-8.1105-27.0144-24.6903
153.59410.08680.47761.9488-1.25591.07410.30080.11580.1593-0.2713-0.07310.08030.1766-0.1906-0.22610.4836-0.003-0.01810.30830.03240.3654-9.4318-13.5749-28.6881
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:4)A1 - 4
2X-RAY DIFFRACTION2(chain A and resid 5:13)A5 - 13
3X-RAY DIFFRACTION3(chain A and resid 14:21)A14 - 21
4X-RAY DIFFRACTION4(chain A and resid 22:64)A22 - 64
5X-RAY DIFFRACTION5(chain A and resid 65:87)A65 - 87
6X-RAY DIFFRACTION6(chain A and resid 88:114)A88 - 114
7X-RAY DIFFRACTION7(chain A and resid 115:135)A115 - 135
8X-RAY DIFFRACTION8(chain B and resid 2:13)B2 - 13
9X-RAY DIFFRACTION9(chain B and resid 14:20)B14 - 20
10X-RAY DIFFRACTION10(chain B and resid 21:52)B21 - 52
11X-RAY DIFFRACTION11(chain B and resid 53:65)B53 - 65
12X-RAY DIFFRACTION12(chain B and resid 66:71)B66 - 71
13X-RAY DIFFRACTION13(chain B and resid 72:87)B72 - 87
14X-RAY DIFFRACTION14(chain B and resid 88:115)B88 - 115
15X-RAY DIFFRACTION15(chain B and resid 116:135)B116 - 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