[English] 日本語
Yorodumi
- PDB-4moq: Pyranose 2-oxidase V546C mutant with 2-fluorinated galactose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4moq
TitlePyranose 2-oxidase V546C mutant with 2-fluorinated galactose
ComponentsPyranose 2-oxidase
KeywordsOXIDOREDUCTASE / GMC OXIDOREDUCTASE / PHBH FOLD / HOMOTETRAMER / FAD-BINDING / SUBSTRATE COMPLEX / FLAVINYLATION / INTRACELLULAR
Function / homology
Function and homology information


pyranose oxidase / pyranose oxidase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / flavin adenine dinucleotide binding / periplasmic space
Similarity search - Function
Phage tail proteins - 2 layer sandwich fold - #50 / Pyranose 2-oxidase / Phage tail proteins - 2 layer sandwich fold / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-deoxy-2-fluoro-beta-D-galactopyranose / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Pyranose 2-oxidase
Similarity search - Component
Biological speciesTrametes ochracea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTan, T.C. / Spadiut, O. / Gandini, R. / Haltrich, D. / Divne, C.
CitationJournal: Plos One / Year: 2014
Title: Structural Basis for Binding of Fluorinated Glucose and Galactose to Trametes multicolor Pyranose 2-Oxidase Variants with Improved Galactose Conversion.
Authors: Tan, T.C. / Spadiut, O. / Gandini, R. / Haltrich, D. / Divne, C.
History
DepositionSep 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyranose 2-oxidase
B: Pyranose 2-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,4338
Polymers141,1162
Non-polymers2,3176
Water20,4471135
1
A: Pyranose 2-oxidase
B: Pyranose 2-oxidase
hetero molecules

A: Pyranose 2-oxidase
B: Pyranose 2-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,86616
Polymers282,2324
Non-polymers4,63412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area25140 Å2
ΔGint-117 kcal/mol
Surface area81710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.724, 101.724, 251.284
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Pyranose 2-oxidase / Pyranose oxidase


Mass: 70558.070 Da / Num. of mol.: 2 / Mutation: V546C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes ochracea (fungus) / Gene: p2o / Plasmid: pET21(d+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7ZA32, pyranose oxidase
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Sugar ChemComp-2FG / 2-deoxy-2-fluoro-beta-D-galactopyranose


Type: D-saccharide, beta linking / Mass: 182.147 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H11FO5
IdentifierTypeProgram
b-D-Galp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1135 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS IS A CLONING ARTIFACT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1 M MES, 50 mM MgCl2, 10% (w/v) monomethylether PEG 2000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2013 / Details: Rh coated meridionally focussing mirror
RadiationMonochromator: Fixed-exit LN2 cooled double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→47.32 Å / Num. all: 173572 / Num. obs: 173572 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 25.3 % / Net I/σ(I): 14.1
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 25.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 28468 / % possible all: 100

-
Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→47.32 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.383 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 1737 1 %RANDOM
Rwork0.18151 ---
all0.18181 171834 --
obs0.18181 171834 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.532 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9008 0 154 1135 10297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.029461
X-RAY DIFFRACTIONr_bond_other_d0.0010.026373
X-RAY DIFFRACTIONr_angle_refined_deg2.1521.96612887
X-RAY DIFFRACTIONr_angle_other_deg1.101315525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89751157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87824.501451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.698151518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4371554
X-RAY DIFFRACTIONr_chiral_restr0.1840.21410
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02110475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021909
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 112 -
Rwork0.339 11806 -
obs--99.99 %
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)
10.1485-0.10580.10570.2374-0.0990.10940.01380.0045-0.0194-0.0137-0.00680.01780.02570.0124-0.0070.0342-0.00120.00220.036-0.00170.00463.91019.8958-24.5007
20.56120.1773-0.13280.3895-0.09640.3402-0.0010.0088-0.0069-0.02070.00610.0406-0.0087-0.0184-0.00510.07450.007-0.0240.05660.00250.0205-9.877717.8262-33.2014
31.032-0.04220.03040.98790.00631.6858-0.0157-0.0050.12060.03790.0092-0.1574-0.16030.2730.00650.0581-0.0142-0.00480.06630.01260.04710.949927.9552-28.7323
40.94220.78230.15771.18830.07650.39010.02550.0039-0.08290.0116-0.011-0.03060.0385-0.0074-0.01450.06370.01-0.00030.0524-0.00330.0227-27.75142.5192-15.016
50.28520.0874-0.10580.2933-0.12060.34930.01090.01030.0188-0.0071-0.0063-0.0211-0.01410.0291-0.00450.05110.002-0.00620.0407-0.00060.0116-1.93625.4726-23.1704
60.3069-0.1094-0.21380.30840.04990.25010.01130.0493-0.0304-0.0448-0.02250.0112-0.004-0.02910.01120.05180.0032-0.02530.0466-0.01220.0236-4.5626-11.9607-24.7812
70.54720.11830.16070.47380.10370.3776-0.00210.0448-0.0567-0.0586-0.0113-0.00260.03860.03870.01340.06690.00910.01240.0449-0.01750.022913.4801-20.3439-30.8695
81.2113-0.12640.38721.00050.02491.63040.01740.0111-0.1636-0.0631-0.0030.3210.1503-0.1883-0.01440.0378-0.0131-0.02930.0459-0.02610.139-12.214-27.5192-30.8108
90.89320.6438-0.19611.1742-0.08030.44040.0184-0.01170.08110.0054-0.01560.0198-0.05440.0287-0.00280.06840.0048-0.00550.0640.00310.017227.7295-3.7615-13.7383
100.41340.06190.12020.41780.09850.3750.00450.0375-0.0919-0.05170.00120.06340.0289-0.0153-0.00570.0477-0.0012-0.00640.0241-0.01410.03662.1062-27.2001-21.6448
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 173
2X-RAY DIFFRACTION2A174 - 308
3X-RAY DIFFRACTION3A309 - 358
4X-RAY DIFFRACTION4A359 - 474
5X-RAY DIFFRACTION5A475 - 618
6X-RAY DIFFRACTION6B43 - 169
7X-RAY DIFFRACTION7B170 - 293
8X-RAY DIFFRACTION8B294 - 358
9X-RAY DIFFRACTION9B359 - 471
10X-RAY DIFFRACTION10B472 - 618

+
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