[English] 日本語
Yorodumi
- PDB-5ns6: Crystal structure of beta-glucosidase BglM-G1 from marine metagenome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ns6
TitleCrystal structure of beta-glucosidase BglM-G1 from marine metagenome
ComponentsBeta-glucosidase
KeywordsHYDROLASE / beta-glucosidase / metagenomes
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesmarine metagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsMhaindarkar, D.C. / Gasper, R. / Lupilova, N. / Leichert, L.I. / Hofmann, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council281384-FuMe Germany
CitationJournal: Commun Biol / Year: 2018
Title: Loss of a conserved salt bridge in bacterial glycosyl hydrolase BgIM-G1 improves substrate binding in temperate environments.
Authors: Mhaindarkar, D. / Gasper, R. / Lupilov, N. / Hofmann, E. / Leichert, L.I.
History
DepositionApr 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _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
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Beta-glucosidase
B: Beta-glucosidase
C: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,82137
Polymers155,6463
Non-polymers3,17534
Water15,475859
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-138 kcal/mol
Surface area45560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.020, 138.020, 97.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 23 or resid 25...
21(chain B and (resid 2 through 23 or resid 25...
31(chain C and (resid 2 through 23 or resid 25...

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
11LYSLYSALAALA(chain A and (resid 2 through 23 or resid 25...AA2 - 2317 - 38
12GLNGLNGLYGLY(chain A and (resid 2 through 23 or resid 25...AA25 - 8740 - 102
13GLYGLYASNASN(chain A and (resid 2 through 23 or resid 25...AA89 - 92104 - 107
14GLUGLUMETMET(chain A and (resid 2 through 23 or resid 25...AA94 - 96109 - 111
15PHEPHELEULEU(chain A and (resid 2 through 23 or resid 25...AA98 - 107113 - 122
16ARGARGGLNGLN(chain A and (resid 2 through 23 or resid 25...AA109 - 124124 - 139
17LEULEUALAALA(chain A and (resid 2 through 23 or resid 25...AA126 - 142141 - 157
18TYRTYRSERSER(chain A and (resid 2 through 23 or resid 25...AA144 - 145159 - 160
19LYSLYSTRPTRP(chain A and (resid 2 through 23 or resid 25...AA147 - 159162 - 174
110THRTHRVALVAL(chain A and (resid 2 through 23 or resid 25...AA161 - 177176 - 192
111ALAALAALAALA(chain A and (resid 2 through 23 or resid 25...AA179 - 191194 - 206
112HISHISILEILE(chain A and (resid 2 through 23 or resid 25...AA193 - 206208 - 221
113GLUGLUSERSER(chain A and (resid 2 through 23 or resid 25...AA208 - 211223 - 226
114LEULEUALAALA(chain A and (resid 2 through 23 or resid 25...AA213 - 326228 - 341
115SERSERGLUGLU(chain A and (resid 2 through 23 or resid 25...AA328 - 334343 - 349
116VALVALALAALA(chain A and (resid 2 through 23 or resid 25...AA336 - 378351 - 393
117PHEPHETYRTYR(chain A and (resid 2 through 23 or resid 25...AA380 - 392395 - 407
118ALAALASERSER(chain A and (resid 2 through 23 or resid 25...AA394 - 439409 - 454
21LYSLYSALAALA(chain B and (resid 2 through 23 or resid 25...BB2 - 2317 - 38
22GLNGLNGLYGLY(chain B and (resid 2 through 23 or resid 25...BB25 - 8740 - 102
23GLYGLYASNASN(chain B and (resid 2 through 23 or resid 25...BB89 - 92104 - 107
24GLUGLUMETMET(chain B and (resid 2 through 23 or resid 25...BB94 - 96109 - 111
25PHEPHELEULEU(chain B and (resid 2 through 23 or resid 25...BB98 - 107113 - 122
26ARGARGGLNGLN(chain B and (resid 2 through 23 or resid 25...BB109 - 124124 - 139
27LEULEUALAALA(chain B and (resid 2 through 23 or resid 25...BB126 - 142141 - 157
28TYRTYRSERSER(chain B and (resid 2 through 23 or resid 25...BB144 - 145159 - 160
29LYSLYSTRPTRP(chain B and (resid 2 through 23 or resid 25...BB147 - 159162 - 174
210THRTHRVALVAL(chain B and (resid 2 through 23 or resid 25...BB161 - 177176 - 192
211ALAALAALAALA(chain B and (resid 2 through 23 or resid 25...BB179 - 191194 - 206
212HISHISILEILE(chain B and (resid 2 through 23 or resid 25...BB193 - 206208 - 221
213GLUGLUSERSER(chain B and (resid 2 through 23 or resid 25...BB208 - 211223 - 226
214LEULEUALAALA(chain B and (resid 2 through 23 or resid 25...BB213 - 326228 - 341
215SERSERGLUGLU(chain B and (resid 2 through 23 or resid 25...BB328 - 334343 - 349
216VALVALALAALA(chain B and (resid 2 through 23 or resid 25...BB336 - 378351 - 393
217PHEPHETYRTYR(chain B and (resid 2 through 23 or resid 25...BB380 - 392395 - 407
218ALAALASERSER(chain B and (resid 2 through 23 or resid 25...BB394 - 439409 - 454
31LYSLYSALAALA(chain C and (resid 2 through 23 or resid 25...CC2 - 2317 - 38
32GLNGLNGLYGLY(chain C and (resid 2 through 23 or resid 25...CC25 - 8740 - 102
33GLYGLYASNASN(chain C and (resid 2 through 23 or resid 25...CC89 - 92104 - 107
34GLUGLUMETMET(chain C and (resid 2 through 23 or resid 25...CC94 - 96109 - 111
35PHEPHELEULEU(chain C and (resid 2 through 23 or resid 25...CC98 - 107113 - 122
36ARGARGGLNGLN(chain C and (resid 2 through 23 or resid 25...CC109 - 124124 - 139
37LEULEUALAALA(chain C and (resid 2 through 23 or resid 25...CC126 - 142141 - 157
38TYRTYRSERSER(chain C and (resid 2 through 23 or resid 25...CC144 - 145159 - 160
39LYSLYSTRPTRP(chain C and (resid 2 through 23 or resid 25...CC147 - 159162 - 174
310THRTHRVALVAL(chain C and (resid 2 through 23 or resid 25...CC161 - 177176 - 192
311ALAALAALAALA(chain C and (resid 2 through 23 or resid 25...CC179 - 191194 - 206
312HISHISILEILE(chain C and (resid 2 through 23 or resid 25...CC193 - 206208 - 221
313GLUGLUSERSER(chain C and (resid 2 through 23 or resid 25...CC208 - 211223 - 226
314LEULEUALAALA(chain C and (resid 2 through 23 or resid 25...CC213 - 326228 - 341
315SERSERGLUGLU(chain C and (resid 2 through 23 or resid 25...CC328 - 334343 - 349
316VALVALALAALA(chain C and (resid 2 through 23 or resid 25...CC336 - 378351 - 393
317PHEPHETYRTYR(chain C and (resid 2 through 23 or resid 25...CC380 - 392395 - 407
318ALAALASERSER(chain C and (resid 2 through 23 or resid 25...CC394 - 439409 - 454

-
Components

#1: Protein Beta-glucosidase


Mass: 51882.125 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) marine metagenome (others) / References: beta-glucosidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 859 / 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: 3 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7 / Details: 0.1M Na-HEPES, 2M AmmSO4, 2% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.00238 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00238 Å / Relative weight: 1
ReflectionResolution: 1.5→48.797 Å / Num. obs: 292649 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.586 % / Biso Wilson estimate: 18.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rrim(I) all: 0.145 / Χ2: 1 / Net I/σ(I): 13.31 / Num. measured all: 3976013 / Scaling rejects: 133
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.5413.7052.3821.05215540.2992.474100
1.54-1.5813.5732.0831.24210610.3982.164100
1.58-1.6313.2461.7011.57205000.5141.77100
1.63-1.6812.691.4911.82198490.5921.554100
1.68-1.7313.9631.2182.45192590.7351.264100
1.73-1.7913.8730.9423.26186320.8330.979100
1.79-1.8613.630.6834.56180230.9140.71100
1.86-1.9413.2570.5255.89172980.9450.546100
1.94-2.0213.0240.3588.29166270.9730.373100
2.02-2.1214.1790.27511159150.9850.285100
2.12-2.2414.0730.20714.1150860.9910.215100
2.24-2.3713.9070.16616.96143230.9940.172100
2.37-2.5412.8160.13319.61134410.9950.138100
2.54-2.7414.3680.10924.59125380.9970.113100
2.74-314.2790.08830.02115600.9980.091100
3-3.3513.8060.06638.08104440.9990.069100
3.35-3.8712.610.04946.4292200.9990.051100
3.87-4.7414.1110.04156.3778640.9990.043100
4.74-6.7113.3230.04253.3560580.9990.044100
6.71-48.79713.4360.03460.54339710.03699.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.49 Å48.96 Å
Translation7.49 Å48.96 Å

-
Processing

Software
NameVersionClassification
XSCALE30-Sep-2016data scaling
PHASER2.6.0phasing
PHENIXdev_2621refinement
PDB_EXTRACT3.22data extraction
XDS30-Sep-2016data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OD0

1od0


Resolution: 1.5→48.797 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.12
RfactorNum. reflection% reflection
Rfree0.172 14633 5 %
Rwork0.1502 --
obs0.1513 292645 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 172.91 Å2 / Biso mean: 25.9104 Å2 / Biso min: 11.54 Å2
Refinement stepCycle: final / Resolution: 1.5→48.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10557 0 377 859 11793
Biso mean--58.64 31.43 -
Num. residues----1314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611323
X-RAY DIFFRACTIONf_angle_d0.83315399
X-RAY DIFFRACTIONf_chiral_restr0.0711537
X-RAY DIFFRACTIONf_plane_restr0.0061971
X-RAY DIFFRACTIONf_dihedral_angle_d14.9014138
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7731X-RAY DIFFRACTION6.293TORSIONAL
12B7731X-RAY DIFFRACTION6.293TORSIONAL
13C7731X-RAY DIFFRACTION6.293TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.5170.29594840.284591989682
1.517-1.53490.31594870.280992399726
1.5349-1.55360.29764880.273492759763
1.5536-1.57330.29574840.257191989682
1.5733-1.5940.26984850.244192219706
1.594-1.61580.24084890.225492959784
1.6158-1.63890.2424850.214492139698
1.6389-1.66340.25554880.213992739761
1.6634-1.68930.24244840.202691969680
1.6893-1.7170.22364860.187392369722
1.717-1.74670.21434890.175792909779
1.7467-1.77840.19964860.166592209706
1.7784-1.81260.20444860.159792469732
1.8126-1.84960.18824870.151392489735
1.8496-1.88980.18024850.139692249709
1.8898-1.93380.17374880.133192689756
1.9338-1.98220.16394860.125792219707
1.9822-2.03580.15074890.121693099798
2.0358-2.09570.14944860.125192199705
2.0957-2.16330.15124890.122792969785
2.1633-2.24060.15454870.120692469733
2.2406-2.33030.14044870.120592679754
2.3303-2.43640.14574880.120992759763
2.4364-2.56480.14564900.126292989788
2.5648-2.72550.15954890.13392909779
2.7255-2.93590.15964890.142992939782
2.9359-3.23130.17174890.151592949783
3.2313-3.69880.16474910.150293289819
3.6988-4.65950.13874920.134393569848
4.6595-48.82330.17965000.170494809980

+
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