[English] 日本語
Yorodumi
- PDB-7qva: Crystal structure of a bacterial pyranose 2-oxidase in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qva
TitleCrystal structure of a bacterial pyranose 2-oxidase in complex with mangiferin
ComponentsGMC oxidoreductase family protein
KeywordsOXIDOREDUCTASE / flavoprotein / mangiferin / substrate / FAD / bacterial / pyranose-2-oxidase
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
: / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Mangiferin / GMC oxidoreductase family protein
Similarity search - Component
Biological speciesPseudarthrobacter siccitolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBorges, P.T. / Frazao, T. / Taborda, T. / Brissos, V. / Frazao, C. / Martins, L.O.
Funding supportEuropean Union, Portugal, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionB-LigZymes H2020-MSCA-RISE 2018European Union
Foundation for Science and Technology (FCT)PTDC/BII-BBF/29564/2017 Portugal
CitationJournal: Nat Commun / Year: 2023
Title: Mechanistic insights into glycoside 3-oxidases involved in C-glycoside metabolism in soil microorganisms.
Authors: Taborda, A. / Frazao, T. / Rodrigues, M.V. / Fernandez-Luengo, X. / Sancho, F. / Lucas, M.F. / Frazao, C. / Melo, E.P. / Ventura, M.R. / Masgrau, L. / Borges, P.T. / Martins, L.O.
History
DepositionJan 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
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 / _pdbx_audit_support.country

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GMC oxidoreductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7986
Polymers55,3021
Non-polymers1,4965
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-38 kcal/mol
Surface area18270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.650, 78.858, 147.348
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1402-

HOH

-
Components

#1: Protein GMC oxidoreductase family protein


Mass: 55301.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudarthrobacter siccitolerans (bacteria)
Gene: ARTSIC4J27_4061 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A024H8G7
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-HZI / Mangiferin / 2-[(2S,3R,4R,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-1,3,6,7-tetrakis(oxidanyl)xanthen-9-one


Mass: 422.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18O11 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2 M ammonium sulfate and 0.1 M Tris-HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.6→73.7 Å / Num. obs: 14110 / % possible obs: 99.5 % / Redundancy: 6.2 % / CC1/2: 0.985 / Net I/σ(I): 6.99
Reflection shellResolution: 2.6→2.7 Å / Num. unique obs: 2229 / CC1/2: 0.495

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AsP2OX WT

Resolution: 2.6→73.67 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.49 / Stereochemistry target values: LS_WUNIT_K1
Details: THE REFINEMENT CONVERGED TO R-WORK AND R-FREE OF 0.228 AND 0.282, RESPECTIVELY, WITH A R-FREE SET OF 1414 REFLECTIONS. THE FINAL MODEL WAS THEN REFINED VERSUS THE FULL DATA SET.
RfactorNum. reflection% reflection
Rfree0.2137 14108 100 %
Rwork0.2137 14108 -
obs0.2137 14108 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.97 Å2 / Biso mean: 35.4186 Å2 / Biso min: 1.81 Å2
Refinement stepCycle: final / Resolution: 2.6→73.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3456 0 98 122 3676
Biso mean--53.7 20.9 -
Num. residues----457
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.630.34614470.346144789490
2.63-2.660.30124500.3012450900100
2.66-2.690.27414450.2741445890100
2.69-2.720.25454780.2545478956100
2.72-2.760.27084850.2708485970100
2.76-2.80.26144350.2614435870100
2.8-2.840.24424790.2442479958100
2.84-2.880.24014660.2401466932100
2.88-2.920.2634660.263466932100
2.92-2.970.24544590.2454459918100
2.97-3.020.23934750.2393475950100
3.02-3.080.25894620.2589462924100
3.08-3.140.2394530.239453906100
3.14-3.20.24274810.2427481962100
3.2-3.270.22744700.2274470940100
3.27-3.350.2034670.203467934100
3.35-3.430.20084700.2008470940100
3.43-3.520.19754520.1975452904100
3.52-3.630.19474830.1947483966100
3.63-3.740.19794620.1979462924100
3.74-3.880.19454720.194547294499
3.88-4.030.18784640.1878464928100
4.03-4.220.1724820.172482964100
4.22-4.440.15984700.1598470940100
4.44-4.720.15794690.1579469938100
4.72-5.080.17334900.173349098099
5.08-5.590.20094740.2009474948100
5.59-6.40.21374860.2137486972100
6.4-8.050.20814940.2081494988100
8.07-73.670.2075220.207522104498
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)
10.08920.0330.12141.03980.51540.38350.1992-0.1159-0.11980.23610.12420.39480.3901-0.3281-0.03420.215-0.1002-0.0610.18830.07570.24988.33136.159325.8454
25.0946-1.9151-0.90846.26421.75275.8052-0.5546-1.02460.94491.25290.1451-0.20530.2630.34890.28590.4084-0.0392-0.01710.3542-0.07240.262417.30423.773438.1893
36.31570.0065-2.30972.6308-2.74347.64770.54050.01390.97720.6694-0.1111-0.9451-1.04020.94090.18880.2467-0.07120.01570.3812-0.04880.507727.565520.197728.6828
40.52430.13950.56450.8160.99711.5296-0.04770.5414-0.3792-0.12770.091-0.64590.03840.87380.0620.04370.0410.12610.57930.24790.912836.699216.936116.9571
50.29280.02420.46941.7001-0.01471.4616-0.03590.03810.24290.0752-0.0904-0.30020.15030.24350.06180.1591-0.012-0.06090.17950.06660.301317.762421.870817.1571
63.74261.20180.550.9782-0.78161.66540.2871-0.1060.2706-0.3186-0.2310.6581-0.5507-0.7392-0.08840.29990.1235-0.02840.22730.05830.20361.883423.286214.399
72.72980.40690.45524.8964-1.53492.0157-0.0859-0.22840.28540.85040.13710.1419-0.5277-0.26650.01280.21610.0391-0.00230.17820.01450.23937.106239.030816.5611
80.1252-0.2530.28741.0895-0.13390.98240.0503-0.1808-0.22770.09650.05550.21840.3395-0.1995-0.05820.2308-0.083-0.00130.20.05070.29427.52557.525529.3695
93.53370.6342.02794.66974.57619.8818-0.58020.20560.1403-0.31580.38820.06590.6530.9785-0.10960.4491-0.0041-0.04180.2306-0.00240.330118.3751-4.266421.4806
101.3829-0.23980.22412.165-1.12560.90170.09220.066-0.2373-0.1086-0.1299-0.30150.34880.02190.03830.2803-0.0084-0.00570.1503-0.01560.154821.074110.303115.8684
114.2348-5.3516-5.24556.76136.62966.49980.6915-0.72110.3739-0.31510.20090.5815-0.7006-0.8417-0.64370.3488-0.12460.18990.8093-0.0430.735813.16253.970125.9109
122.218-0.9966-1.95872.9937-0.38753.9956-0.1408-0.45370.21720.4620.0548-0.0941-0.10030.36220.12420.18170.0622-0.19840.04710.16540.255314.405535.86313.6613
132.7135-0.48060.50674.0883-0.89552.61470.2455-0.1254-0.2107-0.1965-0.1414-0.36060.17620.3037-0.05440.1013-0.06510.05820.28910.08340.321827.64419.364715.0605
144.0146-0.63663.61336.9643-1.83774.0512-0.61180.24110.1746-1.01550.1243-0.49690.52310.5019-0.25650.30080.05550.17410.36420.02870.352830.384125.57033.92
154.4411-1.8164-1.87416.10190.90554.04530.3120.16250.5-0.0665-0.3266-0.0015-0.0089-0.2435-0.03390.2251-0.0673-0.09040.17550.08440.332422.306643.80911.2351
161.78040.6944-0.16422.8548-1.56461.39360.0498-0.01250.0512-0.4751-0.1924-0.17220.4931-0.22990.06860.3416-0-0.0280.18430.02120.209318.322615.84939.0534
171.6132.66110.47996.00270.72170.4944-0.11280.2815-0.3408-0.3370.50330.050.08490.0559-0.02260.2177-0.0092-0.07430.1470.06720.30154.54379.873612.6176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 5:52)A5 - 52
2X-RAY DIFFRACTION2(chain A and resid 53:68)A53 - 68
3X-RAY DIFFRACTION3(chain A and resid 69:98)A69 - 98
4X-RAY DIFFRACTION4(chain A and resid 99:108)A99 - 108
5X-RAY DIFFRACTION5(chain A and resid 109:141)A109 - 141
6X-RAY DIFFRACTION6(chain A and resid 142:166)A142 - 166
7X-RAY DIFFRACTION7(chain A and resid 167:210)A167 - 210
8X-RAY DIFFRACTION8(chain A and resid 211:235)A211 - 235
9X-RAY DIFFRACTION9(chain A and resid 236:253)A236 - 253
10X-RAY DIFFRACTION10(chain A and resid 254:303)A254 - 303
11X-RAY DIFFRACTION11(chain A and resid 304:308)A304 - 308
12X-RAY DIFFRACTION12(chain A and resid 325:346)A325 - 346
13X-RAY DIFFRACTION13(chain A and resid 347:395)A347 - 395
14X-RAY DIFFRACTION14(chain A and resid 396:407)A396 - 407
15X-RAY DIFFRACTION15(chain A and resid 408:426)A408 - 426
16X-RAY DIFFRACTION16(chain A and resid 427:480)A427 - 480
17X-RAY DIFFRACTION17(chain A and resid 481:509)A481 - 509

+
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