[English] 日本語
Yorodumi
- PDB-5yj7: Structural insight into the beta-GH1 glucosidase BGLN1 from oleag... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yj7
TitleStructural insight into the beta-GH1 glucosidase BGLN1 from oleaginous microalgae Nannochloropsis
ComponentsGlycoside hydrolase
KeywordsHYDROLASE / glycoside hydrolase / beta-1 / 3-glucan / substrate specificity / CARBOHYDRATE
Function / homology
Function and homology information


scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesNannochloris (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsDong, S. / Liu, Y.J. / Zhou, H.X. / Xiao, Y. / Xu, J. / Cui, Q. / Wang, X.Q. / Feng, Y.G.
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Structural insight into a GH1 beta-glucosidase from the oleaginous microalga, Nannochloropsis oceanica.
Authors: Dong, S. / Liu, Y.J. / Zhou, H. / Xiao, Y. / Xu, J. / Cui, Q. / Wang, X. / Feng, Y.
History
DepositionOct 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / entity / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Nov 22, 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: Glycoside hydrolase
B: Glycoside hydrolase
C: Glycoside hydrolase
D: Glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,83410
Polymers233,3864
Non-polymers4496
Water53,4322966
1
A: Glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4793
Polymers58,3461
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4382
Polymers58,3461
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4793
Polymers58,3461
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4382
Polymers58,3461
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.720, 74.750, 102.940
Angle α, β, γ (deg.)105.290, 96.100, 90.320
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Glycoside hydrolase


Mass: 58346.391 Da / Num. of mol.: 4 / Mutation: D141G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nannochloris (plant) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A452CSM4*PLUS, beta-glucosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2966 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6
Details: 0.2 M calcium acetate, 0.1 M sodium MES, pH 6.0, and 16% PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.61→28.04 Å / Num. obs: 216408 / % possible obs: 82.7 % / Redundancy: 1.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.034 / Rrim(I) all: 0.048 / Net I/σ(I): 14.5 / Num. measured all: 421792 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.61-1.641.90.258996452300.8290.2580.3653.440.1
8.82-28.041.80.018221512110.9980.0180.02626.776.1

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
Aimless0.5.15data scaling
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RGL

2rgl


Resolution: 1.61→27.306 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 15.55
RfactorNum. reflection% reflection
Rfree0.1515 2000 -
Rwork0.1342 --
obs0.1344 216354 82.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.33 Å2 / Biso mean: 21.73 Å2 / Biso min: 4.5 Å2
Refinement stepCycle: final / Resolution: 1.61→27.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15492 0 58 2966 18516
Biso mean--26.77 33.78 -
Num. residues----1942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616038
X-RAY DIFFRACTIONf_angle_d1.06521769
X-RAY DIFFRACTIONf_chiral_restr0.0422192
X-RAY DIFFRACTIONf_plane_restr0.0052815
X-RAY DIFFRACTIONf_dihedral_angle_d12.2085777
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.61-1.65030.2227720.18047644771641
1.6503-1.69490.2124870.16679402948951
1.6949-1.74470.19011060.1664113541146061
1.7447-1.8010.1821430.1577153201546383
1.801-1.86540.19181590.1475170941725392
1.8654-1.94010.17941590.1482170031716292
1.9401-2.02830.16611600.1427171551731593
2.0283-2.13520.15241600.1367172071736793
2.1352-2.26890.15121620.1282172351739793
2.2689-2.4440.14191610.1287172641742593
2.444-2.68980.15781600.1318171891734993
2.6898-3.07860.13441600.136170841724492
3.0786-3.87690.14481560.1247167931694991
3.8769-27.30950.1281550.1229166101676590
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)
10.6043-0.0304-0.1330.7083-0.08661.5745-0.0196-0.0383-0.05750.0242-0.0134-0.0537-0.02380.30070.01630.05550.0014-0.01630.10630.00170.0957-13.711272.875-10.1578
20.7467-0.0583-0.20610.7781-0.17011.80720.04450.0230.09080.0390.010.0434-0.38330.0289-0.02710.1316-0.0023-0.00060.052700.1066-21.801986.3822-14.3232
30.7852-0.0404-0.22130.6741-0.14191.59140.01030.066-0.0347-0.1049-0.0277-0.0416-0.04770.22080.01570.0726-0.0098-0.00460.1087-0.0120.0969-12.504475.398-20.596
45.7425-0.388-0.72820.35960.53351.7173-0.1298-0.1719-0.24010.06970.0222-0.1240.12080.4410.11660.09920.0396-0.03290.19770.03760.143-5.99866.5-2.6461
50.95130.166-0.26241.36450.13530.4883-0.08160.32820.1836-0.42730.07440.0653-0.3484-0.11840.03010.2647-0.0125-0.03110.17140.070.1393-48.02251.6664-30.6225
61.20110.3858-0.34291.5657-0.15731.09520.0442-0.2203-0.02170.1831-0.0857-0.0562-0.05170.12880.03020.0878-0.0113-0.01520.09860.01550.0923-42.560643.3794-1.3025
71.09020.3907-0.22051.93650.49621.2168-0.0068-0.0711-0.03870.1182-0.05710.13390.0428-0.0950.05440.057-0.00160.00690.07710.00360.111-55.5438.1946-5.6597
81.3234-0.4876-0.6032.44940.74671.3619-0.0172-0.04140.18770.088-0.03670.3296-0.0825-0.18180.05910.06860.0208-0.00120.1188-0.03280.1849-63.682744.5694-6.7874
90.65840.1641.43891.5310.94193.4441-0.25740.5211-0.0457-0.31530.13410.1936-0.1158-0.30590.12630.1565-0.0651-0.04730.2968-0.01880.1461-60.206735.6961-33.7348
100.94540.3523-0.20960.79890.2470.9012-0.10910.2339-0.0183-0.1110.01660.17880.0223-0.27150.08940.1065-0.0127-0.03180.1727-0.01270.1435-60.788136.6369-24.4051
112.3754-0.4253-0.23851.8511-0.20291.2718-0.05390.21280.1881-0.21540.0431-0.1294-0.09360.01870.05010.1309-0.0213-0.0160.070.0140.0872-42.034547.7427-24.9521
121.6723-0.08540.26311.3183-0.39721.8674-0.0550.06090.038-0.10910.04550.0287-0.0374-0.01950.01270.0802-0.0111-0.01110.04470.00780.0976-43.706644.7942-18.103
132.06880.25070.23492.5427-0.57632.3501-0.0184-0.05220.1688-0.04020.0125-0.0353-0.3360.1187-0.00360.1291-0.04380.00390.0894-0.0060.138-35.041754.7196-16.1561
141.0270.1011-0.12481.03080.03830.5797-0.0111-0.2744-0.19170.436-0.05790.09230.4303-0.06830.04550.4005-0.04210.03560.14710.05790.1468-12.66342.0795-46.7053
151.31290.2263-0.13331.9834-0.11431.5687-0.06790.28330.0257-0.14260.0422-0.02460.015-0.11920.04810.09440.0093-0.01110.13490.01480.0831-6.633350.6183-76.3898
161.16060.0328-0.41480.99820.0851.54770.00760.33930.0894-0.015-0.04340.253-0.0025-0.59390.04060.090.0256-0.02420.29990.01470.161-22.481852.4406-72.067
171.75030.0542-0.0261.39990.1720.80530.14280.06960.17280.2825-0.12590.33690.0293-0.66270.07470.18610.01410.10180.3243-0.02630.2317-29.837856.9218-51.2994
181.72-0.0280.2361.35730.15460.1840.03350.23270.12960.136-0.09660.39580.0936-0.55490.04830.1284-0.01520.06190.4211-0.01750.2028-28.865451.6457-60.7964
192.0914-0.44310.10890.56720.1041.40580.0492-0.09850.20220.314-0.07330.1064-0.0751-0.25620.04720.25030.00310.07860.1678-0.02170.1504-20.067957.582-47.2738
202.31821.1971-0.61811.8888-0.31141.50920.0691-0.2278-0.19050.3003-0.1424-0.10350.17250.03490.09450.21240.00710.00010.08090.00870.0901-6.851645.804-52.6913
212.30721.0858-1.24562.1394-1.25082.5412-0.0151-0.0123-0.03480.1329-0.0618-0.00820.0727-0.03660.0730.13210.0115-0.01340.0558-0.00770.0708-8.086948.8903-59.6512
220.3-1.01750.52914.3131-1.19871.4391-0.0248-0.0802-0.16070.3885-0.0732-0.02730.09080.12430.13820.19440.0385-0.00970.11550.03580.16721.358137.8974-59.1752
230.69990.0547-0.06770.82730.07211.1944-0.0025-0.00790.1064-0.10070.0476-0.0651-0.07770.2286-0.01220.1061-0.01520.02620.1038-0.02480.121221.784495.291-67.7133
241.07290.2063-0.36711.03640.0971.7135-0.03490.0439-0.0363-0.18420.04140.07740.1359-0.00670.00130.1251-0.0013-0.0120.0558-0.00220.093210.660884.0313-71.4749
252.6475-1.0031-1.46812.72861.66462.7424-0.05690.0385-0.2866-0.1237-0.04490.03490.3304-0.00170.10680.16680.0159-0.00070.06210.01040.087913.619774.4819-64.9454
260.7720.3361-0.06291.16860.25711.13060.0412-0.23170.01070.1623-0.0329-0.00690.09280.1235-0.00610.09810.011-0.00360.1712-0.01250.081718.663886.4673-48.1032
271.4441-0.43540.30471.3563-0.30061.333-0.0138-0.03390.1799-0.05530.0343-0.1308-0.10510.29370.00950.1036-0.02730.02910.149-0.04520.113226.604996.965-64.6158
285.5234-0.34010.39381.65650.05242.25160.05080.06320.3234-0.21530.0269-0.2303-0.17760.41790.00530.1819-0.07840.07440.172-0.02220.15829.8512101.0717-75.3042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 115 )A21 - 115
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 318 )A116 - 318
3X-RAY DIFFRACTION3chain 'A' and (resid 319 through 479 )A319 - 479
4X-RAY DIFFRACTION4chain 'A' and (resid 480 through 503 )A480 - 503
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 65 )B22 - 65
6X-RAY DIFFRACTION6chain 'B' and (resid 66 through 155 )B66 - 155
7X-RAY DIFFRACTION7chain 'B' and (resid 156 through 233 )B156 - 233
8X-RAY DIFFRACTION8chain 'B' and (resid 234 through 270 )B234 - 270
9X-RAY DIFFRACTION9chain 'B' and (resid 271 through 294 )B271 - 294
10X-RAY DIFFRACTION10chain 'B' and (resid 295 through 398 )B295 - 398
11X-RAY DIFFRACTION11chain 'B' and (resid 399 through 446 )B399 - 446
12X-RAY DIFFRACTION12chain 'B' and (resid 447 through 476 )B447 - 476
13X-RAY DIFFRACTION13chain 'B' and (resid 477 through 509 )B477 - 509
14X-RAY DIFFRACTION14chain 'C' and (resid 21 through 65 )C21 - 65
15X-RAY DIFFRACTION15chain 'C' and (resid 66 through 155 )C66 - 155
16X-RAY DIFFRACTION16chain 'C' and (resid 156 through 270 )C156 - 270
17X-RAY DIFFRACTION17chain 'C' and (resid 271 through 318 )C271 - 318
18X-RAY DIFFRACTION18chain 'C' and (resid 319 through 348 )C319 - 348
19X-RAY DIFFRACTION19chain 'C' and (resid 349 through 398 )C349 - 398
20X-RAY DIFFRACTION20chain 'C' and (resid 399 through 446 )C399 - 446
21X-RAY DIFFRACTION21chain 'C' and (resid 447 through 476 )C447 - 476
22X-RAY DIFFRACTION22chain 'C' and (resid 477 through 510 )C477 - 510
23X-RAY DIFFRACTION23chain 'D' and (resid 21 through 115 )D21 - 115
24X-RAY DIFFRACTION24chain 'D' and (resid 116 through 233 )D116 - 233
25X-RAY DIFFRACTION25chain 'D' and (resid 234 through 270 )D234 - 270
26X-RAY DIFFRACTION26chain 'D' and (resid 271 through 398 )D271 - 398
27X-RAY DIFFRACTION27chain 'D' and (resid 399 through 479 )D399 - 479
28X-RAY DIFFRACTION28chain 'D' and (resid 480 through 503 )D480 - 503

+
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://pdbjlvh1.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