[English] 日本語
Yorodumi
- PDB-4rje: Aerococcus viridans L-lactate oxidase mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rje
TitleAerococcus viridans L-lactate oxidase mutant
ComponentsLactate oxidase
KeywordsOXIDOREDUCTASE / beta/alpha barrel / TIM barrel / oxidase / FMN
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With oxygen as acceptor / : / fatty acid alpha-oxidation / L-lactate dehydrogenase activity / peroxisome / FMN binding / metal ion binding / plasma membrane
Similarity search - Function
L-lactate oxidase / 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 ...L-lactate oxidase / 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
Chem-FNR / PYRUVIC ACID / L-lactate oxidase
Similarity search - Component
Biological speciesAerococcus viridans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRainer, D. / Nidetzky, B. / Wilson, D.K.
CitationJournal: Febs J. / Year: 2015
Title: The Ala95-to-Gly substitution in Aerococcus viridans l-lactate oxidase revisited - structural consequences at the catalytic site and effect on reactivity with O2 and other electron acceptors.
Authors: Stoisser, T. / Rainer, D. / Leitgeb, S. / Wilson, D.K. / Nidetzky, B.
History
DepositionOct 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Mar 11, 2015Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Lactate oxidase
B: Lactate oxidase
C: Lactate oxidase
D: Lactate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,71115
Polymers163,3394
Non-polymers2,37211
Water16,574920
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19000 Å2
ΔGint-53 kcal/mol
Surface area44840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.593, 124.355, 106.885
Angle α, β, γ (deg.)90.00, 124.29, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-641-

HOH

-
Components

#1: Protein
Lactate oxidase


Mass: 40834.688 Da / Num. of mol.: 4 / Mutation: A95G, T102A, S163G, G232A, R255A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aerococcus viridans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q44467, lactate 2-monooxygenase
#2: Chemical
ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H23N4O9P
#3: Chemical
ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 920 / 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: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Drop contained 1 ul 10 mg/ml LOX in 50 mM potassium phosphate pH 7.0 and 1 ul well. Well contained 50 mM pyruvate, 50 mM Tris (pH 8.0) and 30% PEG, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2011
RadiationMonochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→99 Å / Num. all: 157961 / Num. obs: 155981 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Net I/σ(I): 26.4
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 4.1 / % possible all: 95.1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→10 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.63 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17956 7791 5 %RANDOM
Rwork0.15197 ---
obs0.15336 147348 97.71 %-
all-155981 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.313 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0.01 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11185 0 160 920 12265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911595
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210831
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.96615726
X-RAY DIFFRACTIONr_angle_other_deg0.8573.00224913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7551446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50224.264530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.659151839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2321567
X-RAY DIFFRACTIONr_chiral_restr0.0980.21679
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113323
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022640
X-RAY DIFFRACTIONr_mcbond_it0.9431.3095811
X-RAY DIFFRACTIONr_mcbond_other0.9431.3095810
X-RAY DIFFRACTIONr_mcangle_it1.4121.9567248
X-RAY DIFFRACTIONr_mcangle_other1.4121.9567249
X-RAY DIFFRACTIONr_scbond_it1.5941.4815782
X-RAY DIFFRACTIONr_scbond_other1.5941.4815782
X-RAY DIFFRACTIONr_scangle_other2.4992.1558478
X-RAY DIFFRACTIONr_long_range_B_refined3.67211.20814568
X-RAY DIFFRACTIONr_long_range_B_other3.67211.20914569
LS refinement shellResolution: 1.65→1.691 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 520 -
Rwork0.191 10458 -
obs--96.28 %

+
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://pdbjlvh1.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