[English] 日本語
Yorodumi
- PDB-4jy2: Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jy2
TitleCrystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, native and unliganded form
Components2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
KeywordsOXIDOREDUCTASE / FLAVOENZYME / FAD binding motif / 3-hydroxypyridine-5-carboxylic acid
Function / homology
Function and homology information


FAD binding / monooxygenase activity
Similarity search - Function
: / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / 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
BETA-MERCAPTOETHANOL / FLAVIN-ADENINE DINUCLEOTIDE / 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.935 Å
AuthorsKobayashi, J. / Yoshida, H. / Kamitori, S. / Hayashi, H. / Mizutani, K. / Takahashi, N. / Mikami, B. / Yagi, T.
CitationJournal: To be Published
Title: Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
Authors: Kobayashi, J. / Yoshida, H. / Kamitori, S. / Hayashi, H. / Mizutani, K. / Takahashi, N. / Mikami, B. / Yagi, T.
History
DepositionMar 28, 2013Deposition site: RCSB / Processing site: PDBJ
SupersessionApr 2, 2014ID: 3ALH
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
B: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,33717
Polymers83,5972
Non-polymers2,74015
Water11,476637
1
A: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2159
Polymers41,7981
Non-polymers1,4168
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1238
Polymers41,7981
Non-polymers1,3247
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.738, 129.364, 89.302
Angle α, β, γ (deg.)90.00, 122.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-529-

HOH

21A-713-

HOH

31A-714-

HOH

41B-710-

HOH

51B-711-

HOH

61B-712-

HOH

DetailsBIOLOGICAL UNIT IS TETRAMER, BUT SPECIFIC INTERACTION FOR FORMING TETRAMER IS NOT OBSERVED.

-
Components

#1: Protein 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase


Mass: 41798.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: mlr6788 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q988D3, EC: 1.14.12.4
#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: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 8% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.935→50 Å / Num. obs: 78611 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.81 Å2 / Rmerge(I) obs: 0.099
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.308 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.935→49.067 Å / Occupancy max: 1 / Occupancy min: 0.12 / SU ML: 0.15 / σ(F): 1.36 / Phase error: 19.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 3955 5.03 %Random
Rwork0.1677 ---
obs0.1694 78588 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.22 Å2 / Biso mean: 17.9298 Å2 / Biso min: 5.47 Å2
Refinement stepCycle: LAST / Resolution: 1.935→49.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5750 0 180 637 6567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076177
X-RAY DIFFRACTIONf_angle_d1.4168405
X-RAY DIFFRACTIONf_dihedral_angle_d13.3462271
X-RAY DIFFRACTIONf_chiral_restr0.08905
X-RAY DIFFRACTIONf_plane_restr0.0051066
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9349-1.95850.24431290.1958244892
1.9585-1.98330.26441400.19132673100
1.9833-2.00940.20131430.18452617100
2.0094-2.0370.22061340.18382696100
2.037-2.06610.20041190.18152667100
2.0661-2.09690.25041600.17662649100
2.0969-2.12970.20251450.17472717100
2.1297-2.16460.22571540.17612629100
2.1646-2.20190.22751420.16492653100
2.2019-2.24190.20511650.16572641100
2.2419-2.28510.20791310.16452699100
2.2851-2.33170.20761190.1652640100
2.3317-2.38240.2021420.16432684100
2.3824-2.43780.18741330.16762694100
2.4378-2.49880.22071510.1712663100
2.4988-2.56630.20171540.17622678100
2.5663-2.64190.21451400.17172629100
2.6419-2.72710.20951460.17322684100
2.7271-2.82460.21420.17642676100
2.8246-2.93770.22081440.18082686100
2.9377-3.07130.20371460.1732660100
3.0713-3.23320.20991370.17542669100
3.2332-3.43580.19531430.1672702100
3.4358-3.7010.17351360.15972685100
3.701-4.07320.1891240.15262690100
4.0732-4.66220.16461430.14122687100
4.6622-5.87240.18151430.1492691100
5.8724-49.08250.18451500.17652726100

+
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