[English] 日本語
Yorodumi
- PDB-2ad8: crystal structure of methanol dehydrogenase from M. W3A1 (form C)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ad8
Titlecrystal structure of methanol dehydrogenase from M. W3A1 (form C) in the presence of ethanol
Components
  • Methanol dehydrogenase subunit 1
  • Methanol dehydrogenase subunit 2
KeywordsOXIDOREDUCTASE / methanol dehydrogenase / PQQ configuration / ethanol
Function / homology
Function and homology information


methanol dehydrogenase (cytochrome c) / methanol oxidation / alcohol dehydrogenase (cytochrome c(L)) activity / methanol metabolic process / alcohol dehydrogenase (NAD+) activity / outer membrane-bounded periplasmic space / calcium ion binding / plasma membrane
Similarity search - Function
Methanol Dehydrogenase; Chain B / Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit superfamily / Methanol dehydrogenase beta subunit / Quinoprotein alcohol dehydrogenase-like superfamily / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family / Pyrrolo-quinoline quinone repeat ...Methanol Dehydrogenase; Chain B / Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit superfamily / Methanol dehydrogenase beta subunit / Quinoprotein alcohol dehydrogenase-like superfamily / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family / Pyrrolo-quinoline quinone repeat / PQQ-like domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / Few Secondary Structures / Irregular / Mainly Beta
Similarity search - Domain/homology
PYRROLOQUINOLINE QUINONE / Methanol dehydrogenase [cytochrome c] subunit 1 / Methanol dehydrogenase [cytochrome c] subunit 2
Similarity search - Component
Biological speciesMethylophilus methylotrophus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsLi, J. / Gan, J.-H. / Xia, Z.-X. / Mathews, F.S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: The enzymatic reaction-induced configuration change of the prosthetic group PQQ of methanol dehydrogenase
Authors: Li, J. / Gan, J.-H. / Mathews, F.S. / Xia, Z.-X.
History
DepositionJul 20, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Sep 18, 2013Group: Database references
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Methanol dehydrogenase subunit 1
B: Methanol dehydrogenase subunit 2
C: Methanol dehydrogenase subunit 1
D: Methanol dehydrogenase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,2838
Polymers140,5424
Non-polymers7414
Water16,862936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11440 Å2
ΔGint-78 kcal/mol
Surface area40540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.205, 62.630, 124.511
Angle α, β, γ (deg.)90.00, 125.14, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Methanol dehydrogenase subunit 1 / MDH large alpha subunit / MEDH


Mass: 62500.555 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylophilus methylotrophus (bacteria) / Strain: W3A1 / References: UniProt: P38539, EC: 1.1.99.8
#2: Protein Methanol dehydrogenase subunit 2 / MDH small beta subunit / MDH-associated peptide / MEDH


Mass: 7770.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylophilus methylotrophus (bacteria) / Strain: W3A1 / References: UniProt: P38540, EC: 1.1.99.8
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H6N2O8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 936 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / Method: macroseeding / pH: 8.25
Details: Tris-HCl, PEG 8000, ethanol, pH 8.25, macroseeding, temperature 293K

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A
DetectorDetector: CCD / Date: Dec 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 169197 / Num. obs: 157861 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.046
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.219 / Num. unique all: 16796 / % possible all: 68.3

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→42.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 467890.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.195 15403 10 %RANDOM
Rwork0.174 ---
all0.176 169865 --
obs0.174 154407 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.8731 Å2 / ksol: 0.348926 e/Å3
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å2-0.71 Å2
2--3.83 Å20 Å2
3----2.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.6→42.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9894 0 50 936 10880
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.52
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.652.5
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.263 1072 10.3 %
Rwork0.243 9317 -
obs--61.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ccis.paramccis.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5pqq.parampqq.top

+
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