[English] 日本語
Yorodumi
- PDB-8ros: human pyridoxine 5-phosphate oxidase in complex with Z isomer of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ros
Titlehuman pyridoxine 5-phosphate oxidase in complex with Z isomer of pyridoxilidenrhodanine 5-phosphate
ComponentsPyridoxine-5'-phosphate oxidase
KeywordsOXIDOREDUCTASE / Pyrodoxine biosynthesis / Flavoprotein
Function / homology
Function and homology information


pyridoxal 5'-phosphate synthase / pyridoxamine metabolic process / Vitamin B6 activation to pyridoxal phosphate / pyridoxamine phosphate oxidase activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / pyridoxal phosphate binding / FMN binding / protein homodimerization activity / mitochondrion / cytosol
Similarity search - Function
Pyridoxamine 5'-phosphate oxidase, conserved site / Pyridoxamine 5'-phosphate oxidase signature. / Pyridoxamine 5'-phosphate oxidase / Pyridoxine 5'-phosphate oxidase, dimerisation, C-terminal / Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / FMN-binding split barrel
Similarity search - Domain/homology
: / FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Pyridoxine-5'-phosphate oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.553 Å
AuthorsIlari, A. / Fiorillo, A. / Antonelli, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Pyridoxine 5-phosphate oxidase in complex with pyridoxilidenrhodanine 5-phosphate
Authors: Ilari, A. / Fiorillo, A. / Antonelli, L.
History
DepositionJan 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Pyridoxine-5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4416
Polymers30,3871
Non-polymers1,0545
Water3,459192
1
AAA: Pyridoxine-5'-phosphate oxidase
hetero molecules

AAA: Pyridoxine-5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,88312
Polymers60,7752
Non-polymers2,10810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area8570 Å2
ΔGint-43 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.150, 83.150, 59.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein , 1 types, 1 molecules AAA

#1: Protein Pyridoxine-5'-phosphate oxidase / Pyridoxamine-phosphate oxidase


Mass: 30387.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: We have reported the complete sequence but the discrepancies are due to the fact that the N-Terminal portion /1-45 residues) and the loop (residues 236 to 242) are highly mobile and ...Details: We have reported the complete sequence but the discrepancies are due to the fact that the N-Terminal portion /1-45 residues) and the loop (residues 236 to 242) are highly mobile and therefore we were not able to reconstruct these segments.
Source: (gene. exp.) Homo sapiens (human) / Gene: PNPO / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NVS9, pyridoxal 5'-phosphate synthase

-
Non-polymers , 5 types, 197 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-A1H16 / [6-methyl-5-oxidanylidene-4-[(4-oxidanylidene-2-sulfanylidene-1,3-thiazol-5-yl)methyl]-4~{H}-pyridin-3-yl]methyl dihydrogen phosphate


Mass: 362.319 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11N2O6PS2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 12% PEG 6000, 0.1 lithium sulfate, 0.1 sodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.553→45.758 Å / Num. obs: 34420 / % possible obs: 100 % / Redundancy: 18.3 % / CC1/2: 1 / Net I/σ(I): 24.9
Reflection shellResolution: 1.553→1.58 Å / Num. unique obs: 1686 / CC1/2: 0.803

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.553→45.758 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.162 / SU B: 1.569 / SU ML: 0.055 / Average fsc free: 0.9249 / Average fsc work: 0.939 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2004 1675 4.866 %
Rwork0.1627 32745 -
all0.165 --
obs-34420 99.962 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.431 Å2
Baniso -1Baniso -2Baniso -3
1--0.499 Å2-0.25 Å2-0 Å2
2---0.499 Å20 Å2
3---1.62 Å2
Refinement stepCycle: LAST / Resolution: 1.553→45.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 72 192 1978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131865
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171693
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.6572527
X-RAY DIFFRACTIONr_angle_other_deg1.4351.5823917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6895219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65121.786112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87715309
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg24.047151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9211515
X-RAY DIFFRACTIONr_chiral_restr0.0980.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022123
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02452
X-RAY DIFFRACTIONr_nbd_refined0.20.2338
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.21527
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2876
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2897
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2131
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0860.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.212
X-RAY DIFFRACTIONr_nbd_other0.1860.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1470.218
X-RAY DIFFRACTIONr_mcbond_it2.2322.568849
X-RAY DIFFRACTIONr_mcbond_other2.2272.567848
X-RAY DIFFRACTIONr_mcangle_it3.0663.8361062
X-RAY DIFFRACTIONr_mcangle_other3.0663.8361063
X-RAY DIFFRACTIONr_scbond_it3.7562.9711016
X-RAY DIFFRACTIONr_scbond_other3.7542.9721017
X-RAY DIFFRACTIONr_scangle_it5.5514.2981460
X-RAY DIFFRACTIONr_scangle_other5.5494.31461
X-RAY DIFFRACTIONr_lrange_it6.83130.5812129
X-RAY DIFFRACTIONr_lrange_other6.78729.9852090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.553-1.5930.2851270.2582402X-RAY DIFFRACTION99.7633
1.593-1.6370.2581190.2292329X-RAY DIFFRACTION99.9592
1.637-1.6840.2451370.212231X-RAY DIFFRACTION100
1.684-1.7360.2251130.192229X-RAY DIFFRACTION100
1.736-1.7930.221060.1742149X-RAY DIFFRACTION100
1.793-1.8560.1981000.1682069X-RAY DIFFRACTION99.9539
1.856-1.9260.215980.1711995X-RAY DIFFRACTION99.9045
1.926-2.0040.219950.1691931X-RAY DIFFRACTION100
2.004-2.0930.258870.1631858X-RAY DIFFRACTION100
2.093-2.1950.199690.1611806X-RAY DIFFRACTION100
2.195-2.3140.226940.1621672X-RAY DIFFRACTION99.9434
2.314-2.4540.244910.1611592X-RAY DIFFRACTION99.9406
2.454-2.6240.233810.1561503X-RAY DIFFRACTION100
2.624-2.8330.224740.1651421X-RAY DIFFRACTION100
2.833-3.1030.14590.1551300X-RAY DIFFRACTION100
3.103-3.4690.175720.1571180X-RAY DIFFRACTION100
3.469-4.0040.182350.1531065X-RAY DIFFRACTION100
4.004-4.90.152510.135898X-RAY DIFFRACTION100
4.9-6.9140.227450.167697X-RAY DIFFRACTION100
6.914-45.7580.181220.173418X-RAY DIFFRACTION99.7732

+
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