[English] 日本語
Yorodumi
- PDB-6rht: Structure of Pediococcus acidilactici putative lactate oxidase WT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rht
TitleStructure of Pediococcus acidilactici putative lactate oxidase WT protein
ComponentsPutative L-lactate oxidase
KeywordsOXIDOREDUCTASE / FMN alpha-hydroxy acid TIM barrel
Function / homology
Function and homology information


(S)-2-hydroxy-acid oxidase / FMN binding / oxidoreductase activity
Similarity search - Function
Alpha-hydroxy acid dehydrogenase, FMN-dependent / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Alpha-hydroxy acid dehydrogenase, FMN-dependent / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / L-lactate oxidase
Similarity search - Component
Biological speciesPediococcus acidilactici DSM 20284 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAshok, Y. / Maksimainen, M.M. / Kilpelainen, P. / Lehtio, L.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland Finland
CitationJournal: Plos One / Year: 2020
Title: FMN-dependent oligomerization of putative lactate oxidase from Pediococcus acidilactici.
Authors: Ashok, Y. / Maksimainen, M.M. / Kallio, T. / Kilpelainen, P. / Lehtio, L.
History
DepositionApr 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative L-lactate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6367
Polymers39,7191
Non-polymers9176
Water2,198122
1
A: Putative L-lactate oxidase
hetero molecules

A: Putative L-lactate oxidase
hetero molecules

A: Putative L-lactate oxidase
hetero molecules

A: Putative L-lactate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,54228
Polymers158,8754
Non-polymers3,66724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
Buried area19450 Å2
ΔGint-63 kcal/mol
Surface area49060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.240, 135.240, 124.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein Putative L-lactate oxidase


Mass: 39718.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediococcus acidilactici DSM 20284 (bacteria)
Gene: lctO, HMPREF0623_0568 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E0NE46, Oxidoreductases; Acting on the CH-OH group of donors; With unknown physiological acceptors
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 122 / 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: 3.59 Å3/Da / Density % sol: 65.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1.1 M Sodium Malonate, 0.1 M Hepes pH 7.0, 0.5% Jeffamine ED-2003

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→95.63 Å / Num. obs: 45969 / % possible obs: 99.9 % / Redundancy: 8.9 % / Net I/σ(I): 10.3
Reflection shellResolution: 1.928→1.895 Å / Num. unique obs: 2251

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J6X

2j6x


Resolution: 1.9→91.9 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.419 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.113 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22093 2311 5 %RANDOM
Rwork0.18993 ---
obs0.19145 43658 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.168 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å2-0 Å2
2---1.97 Å20 Å2
3---3.93 Å2
Refinement stepCycle: LAST / Resolution: 1.9→91.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 61 122 2970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133005
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172812
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.6514067
X-RAY DIFFRACTIONr_angle_other_deg1.371.5846547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7425387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93524.247146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82815505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5181513
X-RAY DIFFRACTIONr_chiral_restr0.0740.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023382
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02567
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9592.7541527
X-RAY DIFFRACTIONr_mcbond_other1.9542.7521526
X-RAY DIFFRACTIONr_mcangle_it2.8234.1171906
X-RAY DIFFRACTIONr_mcangle_other2.8274.1191907
X-RAY DIFFRACTIONr_scbond_it3.4353.2131478
X-RAY DIFFRACTIONr_scbond_other3.4343.2151479
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2454.6272157
X-RAY DIFFRACTIONr_long_range_B_refined6.68632.4363351
X-RAY DIFFRACTIONr_long_range_B_other6.65332.4043338
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.895→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 161 -
Rwork0.307 3178 -
obs--99.91 %

+
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