[English] 日本語
Yorodumi
- PDB-5oc2: Crystal structure of Asp295Cys/Lys303Cys Amadoriase I mutant from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oc2
TitleCrystal structure of Asp295Cys/Lys303Cys Amadoriase I mutant from Aspergillus Fumigatus
ComponentsFructosyl amine:oxygen oxidoreductase
KeywordsOXIDOREDUCTASE / thermoresistance / flavin dependant enzyme / glycated aminoacid
Function / homology
Function and homology information


fructosyl-amino acid oxidase activity / saccharopine oxidase activity / sarcosine oxidase activity / flavin adenine dinucleotide binding
Similarity search - Function
MTOX family / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-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 / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Fructosyl amine:oxygen oxidoreductase / Fructosyl amine:oxygen oxidoreductase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsRigoldi, F. / Donini, S. / Gautieri, A. / Parisini, E.
Funding support Italy, 1items
OrganizationGrant numberCountry
Cariplo Foundation2013-0766 and 2016-0481 Italy
CitationJournal: Sci Rep / Year: 2018
Title: Thermal stabilization of the deglycating enzyme Amadoriase I by rational design.
Authors: Rigoldi, F. / Donini, S. / Giacomina, F. / Sorana, F. / Redaelli, A. / Bandiera, T. / Parisini, E. / Gautieri, A.
History
DepositionJun 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 23, 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
B: Fructosyl amine:oxygen oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1694
Polymers102,5982
Non-polymers1,5712
Water5,080282
1
A: Fructosyl amine:oxygen oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0842
Polymers51,2991
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fructosyl amine:oxygen oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0842
Polymers51,2991
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.853, 90.462, 81.307
Angle α, β, γ (deg.)90.00, 102.89, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Fructosyl amine:oxygen oxidoreductase


Mass: 51298.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O42629, UniProt: Q4WIF5*PLUS
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate pH 5.6 14% Peg4K 5 % dimethyl sulfoxide

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→48.82 Å / Num. obs: 22860 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.165 / Net I/av σ(I): 10.6 / Net I/σ(I): 10.59
Reflection shellResolution: 2.85→3 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 3316 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wct

4wct


Resolution: 2.85→46.371 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 1150 5.04 %
Rwork0.1718 --
obs0.1756 22838 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→46.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6892 0 106 282 7280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087211
X-RAY DIFFRACTIONf_angle_d1.239807
X-RAY DIFFRACTIONf_dihedral_angle_d15.2992647
X-RAY DIFFRACTIONf_chiral_restr0.0761033
X-RAY DIFFRACTIONf_plane_restr0.0061278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8501-2.97980.28611570.18892669X-RAY DIFFRACTION100
2.9798-3.13680.30091320.1832719X-RAY DIFFRACTION100
3.1368-3.33330.26511310.17992691X-RAY DIFFRACTION100
3.3333-3.59060.251320.1712726X-RAY DIFFRACTION100
3.5906-3.95170.25941440.16062700X-RAY DIFFRACTION100
3.9517-4.52320.21441470.14882709X-RAY DIFFRACTION100
4.5232-5.69710.22091480.17012724X-RAY DIFFRACTION100
5.6971-46.37680.22461590.19352750X-RAY DIFFRACTION100

+
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