[English] 日本語
Yorodumi
- PDB-6a3g: Levoglucosan dehydrogenase, complex with NADH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6a3g
TitleLevoglucosan dehydrogenase, complex with NADH
ComponentsPutative dehydrogenase
KeywordsOXIDOREDUCTASE / NADH-dependent dehydrogenase / Rossmann Fold / Gfo/Idh/MocA family
Function / homology
Function and homology information


levoglucosan dehydrogenase / oxidoreductase activity / nucleotide binding
Similarity search - Function
: / : / GFO/IDH/MocA C-terminal domain / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...: / : / GFO/IDH/MocA C-terminal domain / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Levoglucosan dehydrogenase
Similarity search - Component
Biological speciesPseudarthrobacter phenanthrenivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSugiura, M. / Yamada, C. / Arakawa, T. / Fushinobu, S.
Citation
Journal: J. Biol. Chem. / Year: 2018
Title: Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase.
Authors: Sugiura, M. / Nakahara, M. / Yamada, C. / Arakawa, T. / Kitaoka, M. / Fushinobu, S.
#1: Journal: Biosci. Biotechnol. Biochem. / Year: 1994
Title: Levoglucosan dehydrogenase involved in the assimilation of levoglucosan in Arthrobacter sp. I-552.
Authors: Nakahara, K. / Kitamura, Y. / Yamagishi, Y. / Shoun, H. / Yasui, T.
History
DepositionJun 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: 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 dehydrogenase
B: Putative dehydrogenase
C: Putative dehydrogenase
D: Putative dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,0018
Polymers177,3394
Non-polymers2,6624
Water13,493749
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20660 Å2
ΔGint-97 kcal/mol
Surface area44710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.742, 93.787, 100.989
Angle α, β, γ (deg.)90.00, 100.97, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Putative dehydrogenase


Mass: 44334.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudarthrobacter phenanthrenivorans (strain DSM 18606 / JCM 16027 / LMG 23796 / Sphe3) (bacteria)
Strain: DSM 18606 / JCM 16027 / LMG 23796 / Sphe3 / Gene: Asphe3_10730 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: F0M433
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES-NaOH, PEG 3000, PEG 200, NADH

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 20, 2015
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 114689 / % possible obs: 98.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5628 / CC1/2: 0.903 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H3V

4h3v


Resolution: 1.9→36.53 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.922 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.134 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20448 5652 4.9 %RANDOM
Rwork0.16866 ---
obs0.17046 109019 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.468 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.9→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11461 0 176 749 12386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01411944
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710507
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.67116254
X-RAY DIFFRACTIONr_angle_other_deg1.0021.64424548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.15151481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77321.846623
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.329151798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0731580
X-RAY DIFFRACTIONr_chiral_restr0.0690.21574
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213575
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022325
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_it1.5472.2665948
X-RAY DIFFRACTIONr_mcbond_other1.5462.2655947
X-RAY DIFFRACTIONr_mcangle_it2.1883.3857421
X-RAY DIFFRACTIONr_mcangle_other2.1883.3857422
X-RAY DIFFRACTIONr_scbond_it2.2182.4885996
X-RAY DIFFRACTIONr_scbond_other2.2182.4885997
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3383.6488834
X-RAY DIFFRACTIONr_long_range_B_refined4.35426.99113439
X-RAY DIFFRACTIONr_long_range_B_other4.30826.83713324
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 426 -
Rwork0.258 7792 -
obs--95.86 %

+
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