[English] 日本語
Yorodumi
- PDB-6a6t: Crystal structure of the modified fructosyl peptide oxidase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6a6t
TitleCrystal structure of the modified fructosyl peptide oxidase from Aspergillus nidulans with R61G mutation
ComponentsFructosyl amine: oxygen oxidoreductase
KeywordsOXIDOREDUCTASE / fructosyl peptide / Aspergillus nidulans / FAD-binding protein
Function / homologyD-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Alpha Beta / (4S,5S)-1,2-DITHIANE-4,5-DIOL / FLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesAspergillus nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsOgawa, N. / Maruyama, Y. / Itoh, T. / Hashimoto, W. / Murata, K.
CitationJournal: Sci Rep / Year: 2019
Title: Creation of haemoglobin A1c direct oxidase from fructosyl peptide oxidase by combined structure-based site specific mutagenesis and random mutagenesis.
Authors: Ogawa, N. / Kimura, T. / Umehara, F. / Katayama, Y. / Nagai, G. / Suzuki, K. / Aisaka, K. / Maruyama, Y. / Itoh, T. / Hashimoto, W. / Murata, K. / Ichimura, M.
History
DepositionJun 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructosyl amine: oxygen oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,55211
Polymers48,6211
Non-polymers1,93110
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-67 kcal/mol
Surface area17300 Å2
Unit cell
Length a, b, c (Å)72.349, 72.349, 160.114
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Fructosyl amine: oxygen oxidoreductase


Mass: 48621.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans (mold) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H8O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.4
Details: 1.75 M ammonium sulfate, 0.2 M lithium sulfate, and 0.08 M CAPS (N-cyclohexyl-3-aminopropanesulfonic acid) buffer (pH 10.4)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 38889 / % possible obs: 99.6 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.1
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.405 / Num. unique obs: 1893

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A6R

6a6r


Resolution: 1.901→33.732 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.76
RfactorNum. reflection% reflection
Rfree0.2635 1828 4.72 %
Rwork0.2299 --
obs0.2315 38699 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.901→33.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 113 159 3639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073575
X-RAY DIFFRACTIONf_angle_d1.424849
X-RAY DIFFRACTIONf_dihedral_angle_d13.4251304
X-RAY DIFFRACTIONf_chiral_restr0.059516
X-RAY DIFFRACTIONf_plane_restr0.006607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9013-1.95280.38561360.32822790X-RAY DIFFRACTION99
1.9528-2.01020.35851310.33752800X-RAY DIFFRACTION99
2.0102-2.07510.40441680.31042773X-RAY DIFFRACTION99
2.0751-2.14920.35281400.2822781X-RAY DIFFRACTION100
2.1492-2.23530.34621430.282815X-RAY DIFFRACTION99
2.2353-2.3370.34051250.27332822X-RAY DIFFRACTION99
2.337-2.46020.27561390.26662804X-RAY DIFFRACTION99
2.4602-2.61420.30211410.25662832X-RAY DIFFRACTION99
2.6142-2.8160.29271360.25412816X-RAY DIFFRACTION99
2.816-3.09920.30351580.24962844X-RAY DIFFRACTION100
3.0992-3.54720.23111170.21682901X-RAY DIFFRACTION100
3.5472-4.46750.20261560.17532838X-RAY DIFFRACTION98
4.4675-33.73760.18971380.19063055X-RAY DIFFRACTION99
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)
12.5350.97780.77051.64080.40670.64230.24930.2686-0.16630.1674-0.03240.05120.54940.3772-0.18170.45470.14530.00390.2617-0.01230.2087-32.52331.1023.1637
20.53210.3315-0.06490.91410.78012.13530.00350.0183-0.10820.18570.0917-0.03860.31180.3102-0.0840.30420.14090.01620.2571-0.01330.2303-29.96020.2178-6.6845
30.65080.1110.72151.13220.01612.9937-0.03670.18480.02980.18970.0892-0.17450.37181.08960.02780.32210.2746-0.05330.5728-0.04270.296-22.00723.3637-8.9067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 80 )
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 234 )
3X-RAY DIFFRACTION3chain 'A' and (resid 235 through 433 )

+
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