[English] 日本語
Yorodumi
- PDB-5ohy: A GH31 family sulfoquinovosidase in complex with aza-sugar inhibi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ohy
TitleA GH31 family sulfoquinovosidase in complex with aza-sugar inhibitor IFGSQ
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
Chem-9VH / : / PHOSPHATE ION / THIOCYANATE ION / Alpha-glucosidase yihQ
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsJin, Y. / Williams, S.J. / Goddard-Borger, E. / Davies, G.J.
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-glucosidase yihQ
B: Alpha-glucosidase yihQ
C: Alpha-glucosidase yihQ
D: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,12730
Polymers300,9304
Non-polymers2,19726
Water32,7511818
1
A: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6986
Polymers75,2321
Non-polymers4655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8809
Polymers75,2321
Non-polymers6488
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8809
Polymers75,2321
Non-polymers6488
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-glucosidase yihQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6696
Polymers75,2321
Non-polymers4375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.290, 168.820, 101.390
Angle α, β, γ (deg.)90.000, 117.070, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Alpha-glucosidase yihQ / alpha-sulfoquinovosidase


Mass: 75232.414 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: SY94_3281 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A083ZKV2, alpha-glucosidase

-
Non-polymers , 6 types, 1844 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS
#5: Chemical
ChemComp-9VH / [(3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)piperidin-3-yl]methanesulfonic acid


Mass: 211.236 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO5S
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1818 / 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: 2.5 Å3/Da / Density % sol: 51.2 %
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.

-
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: 1.77→77.8 Å / Num. obs: 284814 / % possible obs: 99.9 % / Redundancy: 4.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.0817 / Net I/σ(I): 11.9
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 21079 / CC1/2: 0.534 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia23.1data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo

Resolution: 1.77→77.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.102
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 14049 4.9 %RANDOM
Rwork0.1768 ---
obs0.1777 284768 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.55 Å2 / Biso mean: 33.9606 Å2 / Biso min: 13.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å2-0.72 Å2
2--0.09 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.77→77.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20697 0 126 1818 22641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01921477
X-RAY DIFFRACTIONr_bond_other_d00.0219110
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.93129200
X-RAY DIFFRACTIONr_angle_other_deg3.7892.99744068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35652654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70623.0381040
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.034153215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.99915159
X-RAY DIFFRACTIONr_chiral_restr0.1120.23071
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02124395
X-RAY DIFFRACTIONr_gen_planes_other0.0130.024924
X-RAY DIFFRACTIONr_mcbond_it1.5111.07610576
X-RAY DIFFRACTIONr_mcbond_other1.4781.07410570
X-RAY DIFFRACTIONr_mcangle_it2.0831.61213207
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 1011 -
Rwork0.314 20040 -
all-21051 -
obs--99.78 %
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)
111.4503-0.4146-1.53296.844-1.54817.61580.0777-0.3235-0.37610.17610.38720.90850.1448-0.8691-0.4650.08140.0202-0.01310.35920.04120.3895-7.391-13.9559.805
20.65170.04280.09290.8401-0.12121.2707-0.0203-0.19810.01210.16930.05480.1577-0.0311-0.1753-0.03450.20410.0339-0.08140.16660.02020.214411.63-6.42552.408
30.4941-0.0212-0.09860.7175-0.02880.7011-0.02190.0292-0.0196-0.08980.03230.10210.0081-0.0657-0.01030.18010.0014-0.12680.13020.0130.187712.2653.24325.827
418.9964-3.0056-10.367636.306434.804636.37080.85061.18330.74350.0025-0.4379-0.0943-0.3354-0.8753-0.41270.364-0.0225-0.23430.51210.3920.48411.841-10.2214.964
514.57571.5425-2.54124.2916-0.975512.2703-0.02421.45430.243-0.23270.0180.2142-0.17580.16110.00610.45390.0017-0.13760.40990.07350.106417.73480.7064.062
60.82070.1153-0.14110.5482-0.0590.78560.00930.14720.0215-0.17260.0167-0.0249-0.0610.1006-0.02610.2542-0.0256-0.10010.1214-0.00750.154118.96970.8123.383
70.50410.0535-0.12450.6663-0.10140.6695-0.01040.01460.0107-0.07620.0460.09220.0981-0.0903-0.03550.2082-0.0396-0.12580.12070.00920.1799-2.01455.73134.469
81.80120.59450.39183.24580.02652.9554-0.04610.1340.0956-0.27840.04660.4406-0.2206-0.4084-0.00060.17410.0533-0.10440.20920.03110.3184-21.08178.21631.136
923.95380.23389.606315.9754-3.75535.10710.08920.67381.2536-0.0706-0.19540.3004-0.36280.17710.10630.96-0.03950.1510.22510.310.563842.3269.122-11.669
101.2402-0.2826-0.05530.5784-0.46681.35730.03990.07140.13210.1924-0.2643-0.186-0.62310.55670.22440.4459-0.2496-0.19880.24360.11240.134143.05348.087-9.124
110.4010.0759-0.07730.5311-0.12051.3132-0.02430.034-0.0265-0.0205-0.0256-0.0078-0.16670.02280.04990.2291-0.0012-0.12920.15360.00980.141720.96832.945-17.097
121.5720.53420.11274.1713-0.54914.13820.0106-0.11020.26960.23050.01540.5998-0.6037-0.7379-0.02610.26380.1521-0.07430.1942-0.03740.17262.09548.266-0.785
135.3015-2.9471-1.3674.5733.09422.3937-0.10330.22530.4317-0.47720.5718-0.9651-0.42990.4019-0.46860.2094-0.32060.00120.87710.16110.6937-18.81138.651-4.655
140.601-0.4666-0.14411.6925-0.59491.5234-0.19330.27740.24410.0814-0.0652-0.2883-0.33770.57460.25840.2996-0.3526-0.23020.620.25540.2156-35.91437.5516.113
150.94410.03330.24220.602-0.23920.9961-0.10080.2390.03340.0990.0203-0.0728-0.07760.26610.08060.2032-0.0572-0.15930.23040.01830.1341-39.1121.13527.871
1614.5811.3161-2.30993.4192.81848.7649-0.1529-0.2209-0.56420.3906-0.0509-0.19240.74320.18820.20370.19960.0868-0.11360.3001-0.04830.1911-24.625-1.77123.868
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 17
2X-RAY DIFFRACTION2A18 - 210
3X-RAY DIFFRACTION3A211 - 658
4X-RAY DIFFRACTION4A659 - 663
5X-RAY DIFFRACTION5B1 - 17
6X-RAY DIFFRACTION6B18 - 213
7X-RAY DIFFRACTION7B214 - 615
8X-RAY DIFFRACTION8B616 - 661
9X-RAY DIFFRACTION9C1 - 17
10X-RAY DIFFRACTION10C18 - 213
11X-RAY DIFFRACTION11C214 - 617
12X-RAY DIFFRACTION12C618 - 662
13X-RAY DIFFRACTION13D9 - 25
14X-RAY DIFFRACTION14D26 - 209
15X-RAY DIFFRACTION15D210 - 646
16X-RAY DIFFRACTION16D647 - 664

+
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