[English] 日本語
Yorodumi
- PDB-4ha6: Crystal structure of pyridoxine 4-oxidase - pyridoxamine complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ha6
TitleCrystal structure of pyridoxine 4-oxidase - pyridoxamine complex
ComponentsPyridoxine 4-oxidase
KeywordsOXIDOREDUCTASE / Substrate binding domain / FAD binding domain / beta alpha beta fold / substrate access tunnel / ADP binding
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
Glucose Oxidase; domain 3 / Glucose Oxidase, domain 3 / GMC oxidoreductases signature 1. / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain ...Glucose Oxidase; domain 3 / Glucose Oxidase, domain 3 / GMC oxidoreductases signature 1. / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / 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 / Chem-PXM / Pyridoxine 4-oxidase
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.095 Å
AuthorsMugo, A.N. / Kobayashi, J. / Mikami, B. / Yagi, T.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Crystal structure of pyridoxine 4-oxidase from Mesorhizobium loti.
Authors: Mugo, A.N. / Kobayashi, J. / Yamasaki, T. / Mikami, B. / Ohnishi, K. / Yoshikane, Y. / Yagi, T.
History
DepositionSep 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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: Pyridoxine 4-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,33110
Polymers54,7331
Non-polymers1,5989
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Pyridoxine 4-oxidase
hetero molecules

A: Pyridoxine 4-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,66220
Polymers109,4652
Non-polymers3,19718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_444-x-1,y-1/2,-z-1/21
Unit cell
Length a, b, c (Å)62.489, 79.169, 135.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Pyridoxine 4-oxidase /


Mass: 54732.746 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 17-520
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: mll6785, pno / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / References: UniProt: Q5NT46, EC: 1.1.3.12
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PXM / 4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL / PYRIDOXAMINE / Pyridoxamine


Mass: 168.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 3.06 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Hepes Na-salt(pH 7.5) 0.1M, 2-propanol 10%,PEG 4000 24%, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2011
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.095→50 Å / Num. all: 38217 / Num. obs: 38074 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 20.12 Å2 / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.146.40.1329.8194.9
2.14-506.30.5385.7198.5

-
Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T37

3t37


Resolution: 2.095→39.702 Å / Occupancy max: 1 / Occupancy min: 0.21 / SU ML: 0.24 / σ(F): 1.33 / Phase error: 22.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2334 1909 5.01 %
Rwork0.1858 --
obs0.1882 38074 94.66 %
all-38217 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.7735 Å2
Refinement stepCycle: LAST / Resolution: 2.095→39.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3844 0 107 244 4195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084126
X-RAY DIFFRACTIONf_angle_d1.2375614
X-RAY DIFFRACTIONf_dihedral_angle_d16.8211547
X-RAY DIFFRACTIONf_chiral_restr0.079596
X-RAY DIFFRACTIONf_plane_restr0.005740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0948-2.14720.29411540.22192590X-RAY DIFFRACTION97
2.1472-2.20530.28711420.21432590X-RAY DIFFRACTION97
2.2053-2.27010.2841550.21512565X-RAY DIFFRACTION96
2.2701-2.34340.24331280.21052592X-RAY DIFFRACTION96
2.3434-2.42720.26581460.20442545X-RAY DIFFRACTION95
2.4272-2.52430.2361220.19712578X-RAY DIFFRACTION95
2.5243-2.63920.27741480.2062506X-RAY DIFFRACTION93
2.6392-2.77830.23071170.20242546X-RAY DIFFRACTION94
2.7783-2.95230.27761280.20482526X-RAY DIFFRACTION93
2.9523-3.18020.25141260.19752536X-RAY DIFFRACTION93
3.1802-3.50.23051420.17742531X-RAY DIFFRACTION93
3.5-4.00610.18741310.16032570X-RAY DIFFRACTION93
4.0061-5.04560.15961280.14532608X-RAY DIFFRACTION94
5.0456-39.70950.23031420.17952882X-RAY DIFFRACTION98

+
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