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- PDB-5ns7: Crystal structure of beta-glucosidase BglM-G1 mutant H75R from ma... -

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Basic information

Entry
Database: PDB / ID: 5ns7
TitleCrystal structure of beta-glucosidase BglM-G1 mutant H75R from marine metagenome
Componentsbeta-glucosidase M - G1
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 / Resolution: 1.54 Å
AuthorsMhaindarkar, D.C. / Gasper, R. / Lupilova, N. / Leichert, L.I. / Hofmann, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council281384 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 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: beta-glucosidase M - G1
B: beta-glucosidase M - G1
C: beta-glucosidase M - G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,86628
Polymers155,5323
Non-polymers2,33425
Water13,619756
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11280 Å2
ΔGint-117 kcal/mol
Surface area45240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.920, 137.920, 98.040
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 0 through 23 or resid 25...
21(chain B and (resid 0 through 23 or resid 25...
31(chain C and (resid 0 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
11HISHISALAALA(chain A and (resid 0 through 23 or resid 25...AA0 - 2315 - 38
12GLNGLNMETMET(chain A and (resid 0 through 23 or resid 25...AA25 - 9640 - 111
13PHEPHEVALVAL(chain A and (resid 0 through 23 or resid 25...AA98 - 177113 - 192
14ALAALAILEILE(chain A and (resid 0 through 23 or resid 25...AA179 - 206194 - 221
15GLUGLUSERSER(chain A and (resid 0 through 23 or resid 25...AA208 - 211223 - 226
16LEULEUASNASN(chain A and (resid 0 through 23 or resid 25...AA213 - 220228 - 235
17THRTHRALAALA(chain A and (resid 0 through 23 or resid 25...AA222 - 378237 - 393
18PHEPHESERSER(chain A and (resid 0 through 23 or resid 25...AA380 - 439395 - 454
21HISHISALAALA(chain B and (resid 0 through 23 or resid 25...BB0 - 2315 - 38
22GLNGLNMETMET(chain B and (resid 0 through 23 or resid 25...BB25 - 9640 - 111
23PHEPHEVALVAL(chain B and (resid 0 through 23 or resid 25...BB98 - 177113 - 192
24ALAALAILEILE(chain B and (resid 0 through 23 or resid 25...BB179 - 206194 - 221
25GLUGLUSERSER(chain B and (resid 0 through 23 or resid 25...BB208 - 211223 - 226
26LEULEUASNASN(chain B and (resid 0 through 23 or resid 25...BB213 - 220228 - 235
27THRTHRLEULEU(chain B and (resid 0 through 23 or resid 25...BB222 - 288237 - 303
28TYRTYRALAALA(chain B and (resid 0 through 23 or resid 25...BB290 - 378305 - 393
29PHEPHESERSER(chain B and (resid 0 through 23 or resid 25...BB380 - 439395 - 454
31HISHISALAALA(chain C and (resid 0 through 23 or resid 25...CC0 - 2315 - 38
32GLNGLNMETMET(chain C and (resid 0 through 23 or resid 25...CC25 - 9640 - 111
33PHEPHEVALVAL(chain C and (resid 0 through 23 or resid 25...CC98 - 177113 - 192
34ALAALAILEILE(chain C and (resid 0 through 23 or resid 25...CC179 - 206194 - 221
35GLUGLUSERSER(chain C and (resid 0 through 23 or resid 25...CC208 - 211223 - 226
36LEULEUASNASN(chain C and (resid 0 through 23 or resid 25...CC213 - 220228 - 235
37THRTHRLEULEU(chain C and (resid 0 through 23 or resid 25...CC222 - 288237 - 303
38TYRTYRALAALA(chain C and (resid 0 through 23 or resid 25...CC290 - 378305 - 393
39PHEPHESERSER(chain C and (resid 0 through 23 or resid 25...CC380 - 439395 - 454

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Components

#1: Protein beta-glucosidase M - G1


Mass: 51844.121 Da / Num. of mol.: 3 / Mutation: H75R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) marine metagenome (others) / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: beta-glucosidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 756 / 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: 3.11 Å3/Da / Density % sol: 60.4 %
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: 1.54→48.762 Å / Num. obs: 270326 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.809 % / Biso Wilson estimate: 20.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.112 / Χ2: 0.966 / Net I/σ(I): 11.28 / Num. measured all: 1840750 / Scaling rejects: 122
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.54-1.586.1571.8210.89199520.3151.99299.7
1.58-1.626.7811.4061.26193730.4641.52499.8
1.62-1.676.8121.151.59188540.5761.24699.8
1.67-1.726.8510.8872.12183830.7060.96199.9
1.72-1.786.8580.6682.89177830.8140.723100
1.78-1.846.7970.4953.9172830.8870.536100
1.84-1.916.4530.3714.99165390.9280.404100
1.91-1.996.5260.2756.56160560.9540.3100
1.99-2.087.2230.2148.89153680.9770.231100
2.08-2.187.1910.16111.49146700.9860.173100
2.18-2.37.1110.13513.33139900.990.145100
2.3-2.437.0480.11115.75132170.9930.119100
2.43-2.66.7660.09517.75124530.9940.103100
2.6-2.816.2920.0819.84115840.9950.087100
2.81-3.087.170.06924.66106450.9970.074100
3.08-3.447.230.05630.8496590.9980.0699.9
3.44-3.987.0590.04635.7585160.9980.0599.9
3.98-4.876.6190.04137.8972430.9980.045100
4.87-6.896.7120.04237.1156270.9980.046100
6.89-48.7627.3330.03942.6231310.9980.04299.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2621refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→48.762 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.28
RfactorNum. reflection% reflection
Rfree0.1717 13515 5 %
Rwork0.1586 --
obs0.1592 270320 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.92 Å2 / Biso mean: 29.9017 Å2 / Biso min: 14.04 Å2
Refinement stepCycle: final / Resolution: 1.54→48.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10606 0 259 756 11621
Biso mean--65.91 32.26 -
Num. residues----1319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911193
X-RAY DIFFRACTIONf_angle_d0.95515196
X-RAY DIFFRACTIONf_chiral_restr0.0561519
X-RAY DIFFRACTIONf_plane_restr0.0071945
X-RAY DIFFRACTIONf_dihedral_angle_d11.4926499
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8060X-RAY DIFFRACTION9.489TORSIONAL
12B8060X-RAY DIFFRACTION9.489TORSIONAL
13C8060X-RAY DIFFRACTION9.489TORSIONAL
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
1.54-1.55750.32924490.31585569005
1.5575-1.57580.31054430.29884458888
1.5758-1.5950.28194540.276785348988
1.595-1.61520.26784470.262585619008
1.6152-1.63650.27044420.254685078949
1.6365-1.65890.25514590.244785579016
1.6589-1.68260.25494410.23785158956
1.6826-1.70770.22384550.223785308985
1.7077-1.73440.25344470.226584648911
1.7344-1.76280.21624520.205486179069
1.7628-1.79320.21214450.192685028947
1.7932-1.82580.19124510.174485298980
1.8258-1.8610.1834520.168385619013
1.861-1.89890.18584480.16585609008
1.8989-1.94020.19454480.161385108958
1.9402-1.98540.15994550.154485759030
1.9854-2.0350.16614440.147685809024
2.035-2.090.16914570.152685569013
2.09-2.15150.17544480.14885038951
2.1515-2.2210.15294520.140186159067
2.221-2.30040.15254440.13985388982
2.3004-2.39250.14654570.138685719028
2.3925-2.50140.15094500.138585679017
2.5014-2.63320.15724500.143585759025
2.6332-2.79820.16894520.150785769028
2.7982-3.01420.15694500.157885819031
3.0142-3.31750.17664510.158486289079
3.3175-3.79740.15324560.144985839039
3.7974-4.78360.12954550.124686589113
4.7836-48.78650.17694610.156787519212
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)
10.9627-0.0661-0.26730.96690.16820.7303-0.0645-0.13660.03750.10360.0542-0.023-0.05990.09590.03420.1730.0073-0.00840.21310.02150.1524-33.077775.794117.6941
21.04370.0967-0.12821.1380.13720.7088-0.0355-0.1717-0.02360.0727-0.0192-0.1258-0.03770.09630.0330.16040.0171-0.01930.22790.01980.1762-22.460771.538918.5213
31.5428-0.775-0.68143.60382.11342.6821-0.0126-0.1220.21080.0431-0.0182-0.152-0.17250.19110.01650.1921-0.0202-0.02890.20560.02350.173-24.940383.82913.5308
41.2826-0.2578-0.24820.55320.04860.7958-0.0315-0.07510.11540.06210.0317-0.001-0.1259-0.021-0.00480.19850.0114-0.00870.1785-0.00040.1597-40.448486.758213.5968
50.9394-0.0282-0.03411.5018-0.37280.8628-0.03470.0082-0.03290.00450.04250.1889-0.062-0.1134-0.01080.15430.0167-0.00650.19740.01680.1517-53.766878.04598.4673
60.4441-0.17050.37231.8981-0.72590.6372-0.0836-0.02830.02870.19670.08780.12430.0047-0.0611-0.00990.1953-0.00930.03890.22860.02220.2045-55.602764.095219.7765
72.1341-0.26460.44224.3323-1.86673.1691-0.07440.0857-0.0111-0.19750.120.20150.0366-0.1207-0.0460.1550.0030.01780.1759-0.00260.1289-47.415469.55110.8688
80.7160.04260.09280.55250.26121.3375-0.0213-0.0996-0.07580.08540.0082-0.00570.09780.044-0.0020.16530.00930.01830.19580.03250.1743-35.96961.742613.7896
91.64360.32430.31682.59352.08223.9250.0083-0.0713-0.18410.0799-0.0077-0.10650.18140.1-0.0270.13970.02830.01970.18340.0480.1904-26.294159.614713.682
100.5799-0.02760.09921.4484-0.08670.9334-0.0158-0.0655-0.28320.0645-0.0091-0.27180.16930.10280.01020.23110.020.03340.21590.01980.3636-13.132335.2182.611
110.978-0.02480.14731.8301-0.26581.5434-0.0083-0.1192-0.16930.12860.0726-0.25570.13120.1608-0.05080.2160.01570.02120.23490.03490.3504-6.405544.26194.9331
121.3351-0.60560.94553.2904-1.34242.38170.0861-0.2094-0.17880.1605-0.0459-0.19420.15690.0422-0.02910.19120.00850.01140.22870.05590.2763-15.498439.093914.0323
131.03580.22280.14661.61510.19330.50690.0126-0.1011-0.43590.02180.0044-0.14370.2033-0.0009-0.01020.24270.0010.01840.18040.06040.3522-23.069727.51637.6352
141.429-0.0524-0.64592.74512.15194.6946-0.05170.1539-0.278-0.2958-0.02810.06770.1323-0.33890.03220.2374-0.02250.01880.1556-0.01320.2952-28.995931.9509-6.6043
151.7448-0.1473-0.95681.1123-0.08911.8984-0.12330.287-0.4288-0.21790.1748-0.01770.4449-0.1841-0.10420.3734-0.08030.01730.2309-0.07290.4873-32.228719.504-10.4141
161.25420.10450.10511.0271-0.32560.7596-0.06310.1774-0.4389-0.21710.0908-0.06340.2897-0.0651-0.04130.293-0.03740.0380.1824-0.06090.3599-26.83927.8984-10.734
171.72910.08390.29411.0165-0.29510.6673-0.08750.1336-0.1673-0.10830.0141-0.21350.1530.1070.05710.22860.00890.06590.1993-0.01990.2684-13.42641.6285-10.8013
182.157-1.06861.32552.8267-1.38382.7543-0.04720.09250.0204-0.0767-0.0079-0.16750.04770.14840.06180.1896-0.00560.04620.21190.00260.2756-8.617149.5889-7.1813
190.5597-0.3084-0.39970.8689-0.37790.8452-0.02160.09030.1019-0.07240.0301-0.037-0.05590.06370.00030.1846-0.00280.00570.22930.00670.149-4.964875.7917-20.7565
200.77960.0034-0.32510.6030.00120.8244-0.0413-0.0003-0.0260.05040.024-0.07770.03660.12120.02330.16950.00490.01260.2450.01190.18320.448769.8614-14.9436
210.76990.1447-0.10530.6426-0.1760.9211-0.05030.1825-0.0193-0.12950.0472-0.0226-0.01620.04140.0050.1851-0.0110.03210.26940.00320.1645-2.930669.4548-32.5074
221.2413-0.66560.1691.6237-0.21251.07380.00720.3270.0191-0.2264-0.02490.1146-0.0993-0.21960.00620.209-0.0138-0.00830.35050.02070.1649-19.587674.1709-39.8441
231.2532-0.4769-0.32371.03110.2640.67720.00910.36130.0085-0.1386-0.03280.0146-0.025-0.13870.00760.1929-0.0165-0.0030.3080.02010.1328-15.029671.5778-38.7028
240.8153-0.222-0.19581.2289-0.12730.7059-0.00590.23310.0528-0.1478-0.01320.0685-0.0296-0.10940.01510.18490.013-0.00530.29610.03010.169-23.617179.4819-31.546
251.3190.6166-0.06180.91790.14360.85430.01810.04380.1215-0.004-0.01920.0521-0.0597-0.05490.01140.17440.01260.0150.20440.02230.1731-18.301479.9086-15.6242
265.06841.7629-0.90491.9133-0.3461.70580.0617-0.12580.06110.1174-0.05050.072-0.0048-0.06190.00050.14260.00590.01720.15630.01450.1117-15.423777.8825-6.3238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 46 )B2 - 46
2X-RAY DIFFRACTION2chain 'B' and (resid 47 through 69 )B47 - 69
3X-RAY DIFFRACTION3chain 'B' and (resid 70 through 109 )B70 - 109
4X-RAY DIFFRACTION4chain 'B' and (resid 110 through 209 )B110 - 209
5X-RAY DIFFRACTION5chain 'B' and (resid 210 through 298 )B210 - 298
6X-RAY DIFFRACTION6chain 'B' and (resid 299 through 325 )B299 - 325
7X-RAY DIFFRACTION7chain 'B' and (resid 326 through 349 )B326 - 349
8X-RAY DIFFRACTION8chain 'B' and (resid 350 through 416 )B350 - 416
9X-RAY DIFFRACTION9chain 'B' and (resid 417 through 439 )B417 - 439
10X-RAY DIFFRACTION10chain 'A' and (resid 2 through 46 )A2 - 46
11X-RAY DIFFRACTION11chain 'A' and (resid 47 through 69 )A47 - 69
12X-RAY DIFFRACTION12chain 'A' and (resid 70 through 108 )A70 - 108
13X-RAY DIFFRACTION13chain 'A' and (resid 109 through 209 )A109 - 209
14X-RAY DIFFRACTION14chain 'A' and (resid 210 through 230 )A210 - 230
15X-RAY DIFFRACTION15chain 'A' and (resid 231 through 265 )A231 - 265
16X-RAY DIFFRACTION16chain 'A' and (resid 266 through 349 )A266 - 349
17X-RAY DIFFRACTION17chain 'A' and (resid 350 through 416 )A350 - 416
18X-RAY DIFFRACTION18chain 'A' and (resid 417 through 439 )A417 - 439
19X-RAY DIFFRACTION19chain 'C' and (resid 2 through 46 )C2 - 46
20X-RAY DIFFRACTION20chain 'C' and (resid 47 through 108 )C47 - 108
21X-RAY DIFFRACTION21chain 'C' and (resid 109 through 209 )C109 - 209
22X-RAY DIFFRACTION22chain 'C' and (resid 210 through 265 )C210 - 265
23X-RAY DIFFRACTION23chain 'C' and (resid 266 through 298 )C266 - 298
24X-RAY DIFFRACTION24chain 'C' and (resid 299 through 349 )C299 - 349
25X-RAY DIFFRACTION25chain 'C' and (resid 350 through 416 )C350 - 416
26X-RAY DIFFRACTION26chain 'C' and (resid 417 through 439 )C417 - 439

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