[English] 日本語
Yorodumi
- PDB-3k4l: Pyranose 2-oxidase F454N mutant in complex with 2FG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k4l
TitlePyranose 2-oxidase F454N mutant in complex with 2FG
ComponentsPyranose 2-oxidase
KeywordsOXIDOREDUCTASE / GMC OXIDOREDUCTASE / F454N MUTANT / ROSSMANN FOLD / PHBH FOLD / HOMOTETRAMER / 8-ALPHA-(N3) HISTIDYL FLAVINYLATION
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
FLAVIN-ADENINE DINUCLEOTIDE / 2-deoxy-2-fluoro-beta-D-glucopyranose / Pyranose 2-oxidase
Similarity search - Component
Biological speciesTrametes ochracea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDivne, C. / Tan, T.C.
CitationJournal: Febs J. / Year: 2010
Title: Importance of the gating segment in the substrate-recognition loop of pyranose 2-oxidase.
Authors: Spadiut, O. / Tan, T.C. / Pisanelli, I. / Haltrich, D. / Divne, C.
History
DepositionOct 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Nov 1, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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)141,2839
Polymers138,7612
Non-polymers2,5217
Water13,007722
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)282,56518
Polymers277,5234
Non-polymers5,04214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area26730 Å2
ΔGint-96 kcal/mol
Surface area79970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.572, 101.572, 250.052
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: 69380.719 Da / Num. of mol.: 2 / Mutation: F454N
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-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Sugar ChemComp-SHG / 2-deoxy-2-fluoro-beta-D-glucopyranose / 2-deoxy-2-fluoro-beta-D-glucose / 2-deoxy-2-fluoro-D-glucose / 2-deoxy-2-fluoro-glucose


Type: D-saccharide, beta linking / Mass: 182.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11FO5
IdentifierTypeProgram
b-D-Glcp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 722 / 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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1M MES, 50MM 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: MAX II / Beamline: I911-2 / Wavelength: 1.0379 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 5, 2008 / Details: MIRRORS
RadiationMonochromator: BENT SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 132005 / Num. obs: 132005 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rsym value: 0.102 / Net I/σ(I): 15.4
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 10540 / Rsym value: 0.883 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2IGO

2igo


Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.318 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20943 1974 1.5 %RANDOM
Rwork0.17544 ---
all0.17596 130031 --
obs0.17596 130031 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8944 0 166 722 9832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0229346
X-RAY DIFFRACTIONr_bond_other_d0.0020.026298
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.96812712
X-RAY DIFFRACTIONr_angle_other_deg1.036315350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74251130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7424.505444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.301151496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.731554
X-RAY DIFFRACTIONr_chiral_restr0.2220.21389
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210324
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021852
X-RAY DIFFRACTIONr_nbd_refined0.2320.21873
X-RAY DIFFRACTIONr_nbd_other0.2110.26888
X-RAY DIFFRACTIONr_nbtor_refined0.1860.24635
X-RAY DIFFRACTIONr_nbtor_other0.0930.24853
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2586
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2270.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.431.57163
X-RAY DIFFRACTIONr_mcbond_other0.351.52266
X-RAY DIFFRACTIONr_mcangle_it1.68529210
X-RAY DIFFRACTIONr_scbond_it2.80934243
X-RAY DIFFRACTIONr_scangle_it3.8874.53502
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.844 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.282 277 -
Rwork0.219 18697 -
obs--99.93 %
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)
10.0737-0.10160.04830.1872-0.07410.03280.0185-0.0098-0.0142-0.0273-0.00840.01230.0150.0064-0.01020.04590.0036-0.00510.03730.00010.02493.451110.1893-24.6064
20.18090.035-0.07510.111-0.11590.24160.00640.02560.0034-0.04370.01250.0380.0088-0.0324-0.01890.04650.0049-0.02250.0255-0.00030.0207-12.990217.6442-32.5237
30.3426-0.10820.02850.254-0.08450.35890.0120.0104-0.00810.0047-0.0516-0.0542-0.04040.05680.03960.0406-0.00290.0050.03070.01620.034912.075825.1584-31.1189
40.43830.55650.07480.71820.04590.21920.01860.0022-0.0157-0.0099-0.0161-0.01080.011-0.0042-0.00250.03110.0042-0.01250.0242-0.00480.0381-28.72941.7113-14.9897
50.09080.0215-0.07530.1-0.04380.10660.0127-0.00690.0134-0.0035-0.0096-0.0048-0.01270.0006-0.00310.04720.002-0.00570.03310.00540.0295-2.2625.1983-22.9988
60.35390.0054-0.11380.8213-0.23480.10280.040.02040.0175-0.27960.00690.0848-0.0030.046-0.04690.13470.0058-0.0630.0191-0.0377-0.0094-0.4861-18.3294-41.5374
70.0841-0.0783-0.05850.1170.02240.0640.0173-0.0089-0.0312-0.0171-0.01970.0257-0.01330.00670.00240.0376-0.0001-0.01440.0277-0.00690.0471-5.1995-9.2812-16.5424
80.2546-0.01530.12410.4301-0.02410.13990.01080.0014-0.045-0.1403-0.01590.05750.03790.05290.00510.06930.0049-0.0258-0.0032-0.03090.0225.0373-22.7845-30.5624
90.33830.3311-0.13150.5643-0.04220.16980.0053-0.0238-0.0003-0.0186-0.01340.0089-0.02540.01990.00810.0435-0.00350.00090.03060.00530.022328.4476-3.4452-13.5877
100.1190.02350.0990.2707-0.03220.1610.0049-0.0259-0.0542-0.0491-0.00450.06370.02520.0368-0.00030.050.0002-0.01640.0022-0.02170.05472.1221-27.3686-21.7621
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 175
2X-RAY DIFFRACTION2A176 - 293
3X-RAY DIFFRACTION3A294 - 359
4X-RAY DIFFRACTION4A360 - 472
5X-RAY DIFFRACTION5A473 - 618
6X-RAY DIFFRACTION6B46 - 85
7X-RAY DIFFRACTION7B86 - 173
8X-RAY DIFFRACTION8B174 - 361
9X-RAY DIFFRACTION9B362 - 473
10X-RAY DIFFRACTION10B474 - 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