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- PDB-5ns6: Crystal structure of beta-glucosidase BglM-G1 from marine metagenome -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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Phasing

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

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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

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