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- PDB-5ohs: A GH31 family sulfoquinovosidase mutant D455N in complex with pNPSQ -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5ohs
TitleA GH31 family sulfoquinovosidase mutant D455N in complex with pNPSQ
ComponentsAlpha-glucosidase yihQ
KeywordsHYDROLASE / sulfoglycosidase / sulfoglycolysis / complex / general acid-base varient
Function / homology
Function and homology information


maltose alpha-glucosidase activity / alpha-glucosidase / carbohydrate binding
Similarity search - Function
Sulfoquinovosidase YihQ-like / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulin-like ...Sulfoquinovosidase YihQ-like / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / 4-nitrophenyl alpha-D-6-sulfoquinovoside / THIOCYANATE ION / Alpha-glucosidase yihQ
Similarity search - Component
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsJin, Y. / Williams, S.J. / Goddard-Borger, E. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research CouncilAdG-322942 United Kingdom
CitationJournal: ACS Cent Sci / Year: 2018
Title: Structural and Biochemical Insights into the Function and Evolution of Sulfoquinovosidases.
Authors: Abayakoon, P. / Jin, Y. / Lingford, J.P. / Petricevic, M. / John, A. / Ryan, E. / Wai-Ying Mui, J. / Pires, D.E.V. / Ascher, D.B. / Davies, G.J. / Goddard-Borger, E.D. / Williams, S.J.
History
DepositionJul 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / struct
Item: _citation.country / _citation.journal_abbrev ..._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 / _struct.title
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-glucosidase yihQ
B: Alpha-glucosidase yihQ
C: Alpha-glucosidase yihQ
D: Alpha-glucosidase yihQ
E: Alpha-glucosidase yihQ
F: Alpha-glucosidase yihQ
G: Alpha-glucosidase yihQ
H: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)607,71059
Polymers601,8528
Non-polymers5,85951
Water39,0572168
1
A: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,22710
Polymers75,2311
Non-polymers9969
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8756
Polymers75,2311
Non-polymers6435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6984
Polymers75,2311
Non-polymers4663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1169
Polymers75,2311
Non-polymers8858
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8716
Polymers75,2311
Non-polymers6395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,29512
Polymers75,2311
Non-polymers1,06411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8767
Polymers75,2311
Non-polymers6456
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7525
Polymers75,2311
Non-polymers5214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.200, 169.190, 169.690
Angle α, β, γ (deg.)90.000, 92.800, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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Components

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Protein / Sugars , 2 types, 16 molecules ABCDEFGH

#1: Protein
Alpha-glucosidase yihQ


Mass: 75231.438 Da / Num. of mol.: 8 / Mutation: E370A, E371A, D455N,
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: SY94_3281 / Plasmid: pET29 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A083ZKV2, alpha-glucosidase
#6: Sugar
ChemComp-NSQ / 4-nitrophenyl alpha-D-6-sulfoquinovoside


Type: D-saccharide / Mass: 365.313 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H15NO10S

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Non-polymers , 6 types, 2211 molecules

#2: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CNS
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2168 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein stock at 45 mg/mL in the buffer of 50 mM NaPO4 and 500 mM NaCl is mixed with the precipitant of 0.2 M KSCN, 21% PEG3350, 0.1 M bis-Tris propane pH 6.5, at a ratio of 1.2: 1.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.97→75.77 Å / Num. obs: 411803 / % possible obs: 99.8 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0779 / Net I/σ(I): 11.6
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.965 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 30415 / CC1/2: 0.558 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.1data extraction
xia2data reduction
xia2data scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo

Resolution: 1.97→75.77 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 20006 4.9 %RANDOM
Rwork0.181 391797 --
obs0.182 411803 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.4 Å2 / Biso mean: 34.7035 Å2 / Biso min: 4.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20.19 Å2
2---1.03 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.97→75.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41583 0 368 2168 44119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01943123
X-RAY DIFFRACTIONr_bond_other_d00.0238307
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.93758625
X-RAY DIFFRACTIONr_angle_other_deg3.798388348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39955294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81323.1552089
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.038156445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.04415310
X-RAY DIFFRACTIONr_chiral_restr0.1220.26174
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02148939
X-RAY DIFFRACTIONr_gen_planes_other0.0170.029852
X-RAY DIFFRACTIONr_mcbond_it1.0431.60521184
X-RAY DIFFRACTIONr_mcbond_other1.0381.60421175
X-RAY DIFFRACTIONr_mcangle_it1.6292.426458
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 1330 -
Rwork0.331 29074 -
all-30404 -
obs--99.95 %
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)
11.09790.04060.22321.4915-0.39811.37140.021-0.1765-0.20310.16350.04180.06360.2001-0.0072-0.06290.09630.00090.04280.21010.0550.221916.274-14.07247.48
20.64430.03960.03050.9135-0.11660.53360.0045-0.1534-0.04640.16060.00650.03810.08150.0081-0.01110.08740.0080.04560.17110.02330.197812.682-8.06939.521
30.4894-0.2051-0.07870.6962-0.08580.5088-0.0076-0.03080.01910.05480.02730.1191-0.0514-0.0186-0.01970.0554-0.0040.04460.14850.02940.2865-4.0385.90525.298
44.00791.9271-0.60364.2826-0.12632.31470.00090.2391-0.0776-0.4981-0.04280.52090.2204-0.19960.04190.13170.0072-0.04210.196700.2703-0.822-8.3262.809
511.3433-4.91320.48558.49524.68777.41460.276-0.0069-0.6910.22830.218-0.18150.78640.2399-0.49410.25030.03190.04250.0202-0.05420.31535.555-109.12841.435
60.76060.01730.17180.60230.10550.83960.00110.1812-0.1657-0.2132-0.0029-0.0550.1179-0.00640.00170.1165-0.01120.07230.1562-0.04150.234633.736-87.88342.245
70.63280.1466-0.01050.73170.13280.6263-0.00540.0256-0.014-0.0584-0.0033-0.1352-0.04760.03090.00880.0552-0.00660.06640.1577-0.01190.282751.55-73.80958.684
85.7629-2.0722-1.28353.48480.50872.347-0.0622-0.4881-0.29660.4126-0.0291-0.47660.25650.15060.09120.1464-0.0446-0.01310.2120.06330.288648.757-87.88681.298
923.1949-11.2674-3.648822.3461-0.21330.81590.2411-0.59881.13120.5851-0.1048-0.9352-0.11640.0828-0.13620.40010.2066-0.18060.655-0.15160.1804-51.357-30.23439.635
101.1996-0.7616-0.70331.16790.40280.8626-0.1815-0.3360.25890.28440.319-0.30630.14690.0264-0.13750.10450.0796-0.08510.1861-0.10520.2029-50.933-38.05917.847
110.7178-0.6008-0.37571.20960.34510.7434-0.0397-0.15960.33430.03180.2377-0.53710.02110.1423-0.1980.00670.0228-0.00730.1108-0.11770.4154-29.003-48.7452.765
1211.49853.6705-0.82841.77964.000430.30880.20230.3462-0.66830.06550.1479-0.33690.05660.3188-0.35030.13510.05130.0770.2360.02520.7451-6.316-34.11510.14
136.763-1.5314-2.26214.72211.907813.2192-0.03930.31430.2094-0.24050.15950.1355-0.3151-0.5921-0.12020.26320.0147-0.09940.23630.05010.105796.084-110.21147.958
140.7240.1837-0.28520.6171-0.05690.5903-0.02460.15290.0522-0.14350.05680.05140.00140.0324-0.03230.1146-0.0357-0.00690.14130.01010.187898.326-118.07167.578
150.60810.1077-0.05941.0327-0.05530.58390.01070.01340.07940.01470.00530.28910.0234-0.0684-0.0160.0633-0.03470.03670.1322-0.00490.286577.271-128.61783.249
1612.9322-0.8561-5.07935.3347-3.820630.33030.2652-0.2589-0.1440.0260.06790.8133-0.2769-0.6542-0.33310.0646-0.0237-0.04520.19630.00460.465954.658-113.63675.465
178.7342-1.97321.99954.0114-1.6366.0809-0.0510.0882-0.56930.08380.21750.38190.2648-0.2769-0.16660.1793-0.02820.05850.13810.00380.2632-88.829-41.24514.189
180.4711-0.2029-0.20540.68990.00320.6717-0.0381-0.07030.01270.01720.05130.05370.04790.0269-0.01310.11270.00320.00030.13430.00260.179-74.7-30.5934.482
190.50280.1142-0.0881.06960.02310.49370.01090.08130.0746-0.27970.02310.088-0.0402-0.0051-0.03390.1893-0.0097-0.03130.12120.03820.1489-74.362-16.164-19.071
203.4411-0.54460.0143.4083-0.14471.5938-0.01760.3523-0.4262-0.5639-0.00460.45460.0409-0.22250.02220.3115-0.0429-0.1670.1274-0.0520.1586-87.306-39.078-33.296
2110.43622.7263-2.69252.77340.62729.9305-0.13810.0892-0.4736-0.08940.0395-0.44550.53060.37880.09870.11650.05640.07310.1011-0.00520.331139.401-120.39171.101
220.47020.1625-0.25770.54750.13250.7661-0.01970.062-0.0279-0.03140.017-0.1140.0655-0.02310.00270.1116-0.00730.01060.11430.00350.2152123.428-110.69479.733
230.5144-0.046-0.10010.79330.11140.65060.0395-0.09720.00560.13630.0104-0.11020.06330.0669-0.04980.1448-0.0116-0.02730.1489-0.00190.1793124.518-97.87104.776
2415.28570.3585-2.95725.870110.678620.2872-0.04450.0722-0.9493-0.15520.5061-0.385-0.32270.9263-0.46150.40270.0238-0.07310.26660.10750.3115136.857-109.596125.277
258.53373.42092.69438.0217-4.42168.59360.1969-0.8103-0.33891.1077-0.5085-0.168-0.28770.47780.31160.2830.05630.01440.42060.02430.112337.9552.23372.348
260.77020.3285-0.13260.9161-0.32050.84020.0645-0.2746-0.11420.1669-0.0143-0.04490.10940.0813-0.05030.0746-0.00110.00150.242-0.00370.156137.0212.7651.747
270.82530.0068-0.14980.6105-0.16320.70.0357-0.18330.07870.0372-0.018-0.0802-0.01510.1317-0.01770.0273-0.02240.01030.2025-0.0620.232253.78719.3236.473
284.4085-3.04366.672625.2818-16.637628.5558-0.65110.01830.7378-0.35620.6124-0.4088-1.4850.37240.03880.2231-0.1371-0.03910.2709-0.15630.358459.00943.59749.828
297.226-2.13386.02269.07040.48946.00710.2621-0.0194-0.3996-1.4249-0.3510.6112-0.4127-0.46620.0890.51450.1356-0.30560.633-0.25790.26929.292-78.50111.959
300.7426-0.1408-0.07760.86970.1830.6741-0.02210.2081-0.1703-0.18950.04450.03840.1755-0.0319-0.02240.1223-0.04390.01370.1891-0.01320.177710.789-78.15832.845
310.517-0.0173-0.05770.72160.01810.763-0.02230.041-0.0453-0.00110.05860.14520.0482-0.0882-0.03630.041-0.02710.01310.18250.05470.2379-6.484-61.55347.748
328.168-0.42030.544910.40032.633315.7503-0.12350.17220.4016-0.15660.2270.297-0.4236-0.4027-0.10360.16770.0175-0.02940.24530.11090.2282-11.061-39.41730.967
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 65
2X-RAY DIFFRACTION2A66 - 209
3X-RAY DIFFRACTION3A210 - 631
4X-RAY DIFFRACTION4A632 - 661
5X-RAY DIFFRACTION5B1 - 20
6X-RAY DIFFRACTION6B21 - 208
7X-RAY DIFFRACTION7B209 - 631
8X-RAY DIFFRACTION8B632 - 661
9X-RAY DIFFRACTION9C1 - 9
10X-RAY DIFFRACTION10C10 - 211
11X-RAY DIFFRACTION11C212 - 649
12X-RAY DIFFRACTION12C650 - 661
13X-RAY DIFFRACTION13D1 - 17
14X-RAY DIFFRACTION14D18 - 222
15X-RAY DIFFRACTION15D223 - 649
16X-RAY DIFFRACTION16D650 - 661
17X-RAY DIFFRACTION17E1 - 26
18X-RAY DIFFRACTION18E27 - 222
19X-RAY DIFFRACTION19E223 - 615
20X-RAY DIFFRACTION20E616 - 661
21X-RAY DIFFRACTION21F1 - 20
22X-RAY DIFFRACTION22F21 - 224
23X-RAY DIFFRACTION23F225 - 658
24X-RAY DIFFRACTION24F659 - 664
25X-RAY DIFFRACTION25G1 - 20
26X-RAY DIFFRACTION26G21 - 219
27X-RAY DIFFRACTION27G220 - 653
28X-RAY DIFFRACTION28G654 - 661
29X-RAY DIFFRACTION29H1 - 20
30X-RAY DIFFRACTION30H21 - 213
31X-RAY DIFFRACTION31H214 - 646
32X-RAY DIFFRACTION32H647 - 661

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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

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