[English] 日本語
Yorodumi
- PDB-5xm3: Crystal Structure of Methanol dehydrogenase from Methylophaga ami... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xm3
TitleCrystal Structure of Methanol dehydrogenase from Methylophaga aminisulfidivorans
Components
  • Glucose dehydrogenase
  • Methanol dehydrogenase [cytochrome c] subunit 2
KeywordsOXIDOREDUCTASE / marine / methanol dehydrogenase / methylophaga / pyrroloquinoline quinone / Mg++
Function / homology
Function and homology information


methanol dehydrogenase (cytochrome c) / methanol oxidation / alcohol dehydrogenase (cytochrome c(L)) activity / oxidoreductase activity, acting on CH-OH group of donors / alcohol dehydrogenase (NAD+) activity / outer membrane-bounded periplasmic space / calcium ion binding / membrane
Similarity search - Function
Bacterial quinoprotein dehydrogenases signature 1. / Methanol Dehydrogenase; Chain B / Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit superfamily / Methanol dehydrogenase beta subunit / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / Quinoprotein alcohol dehydrogenase-like superfamily / PQQ-dependent dehydrogenase, methanol/ethanol family ...Bacterial quinoprotein dehydrogenases signature 1. / Methanol Dehydrogenase; Chain B / Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit superfamily / Methanol dehydrogenase beta subunit / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / Quinoprotein alcohol dehydrogenase-like superfamily / PQQ-dependent dehydrogenase, methanol/ethanol family / Pyrrolo-quinoline quinone repeat / Outer membrane protein assembly factor BamB / 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 / Glucose dehydrogenase / Methanol dehydrogenase [cytochrome c] subunit 2
Similarity search - Component
Biological speciesMethylophaga aminisulfidivorans MP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsCao, T.P. / Choi, J.M. / Lee, S.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Chosun University2015 Korea, Republic Of
CitationJournal: J. Microbiol. / Year: 2018
Title: The crystal structure of methanol dehydrogenase, a quinoprotein from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT
Authors: Cao, T.P. / Choi, J.M. / Kim, S.W. / Lee, S.H.
History
DepositionMay 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Structure summary
Category: citation / struct / struct_keywords
Item: _citation.journal_issue / _citation.journal_volume ..._citation.journal_issue / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _struct.pdbx_descriptor / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucose dehydrogenase
B: Methanol dehydrogenase [cytochrome c] subunit 2
C: Glucose dehydrogenase
D: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,3508
Polymers158,6414
Non-polymers7094
Water17,601977
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12140 Å2
ΔGint-53 kcal/mol
Surface area40650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.926, 109.479, 95.554
Angle α, β, γ (deg.)90.00, 100.48, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Glucose dehydrogenase / Methanol dehydrogenase large subunit


Mass: 69341.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylophaga aminisulfidivorans MP (bacteria)
Gene: MAMP_01209
Production host: Methylophaga aminisulfidivorans MP (bacteria)
References: UniProt: A3FJ48
#2: Protein Methanol dehydrogenase [cytochrome c] subunit 2 / MDH small subunit beta / MDH-associated peptide / MEDH


Mass: 9978.702 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylophaga aminisulfidivorans MP (bacteria)
Gene: MAMP_01202
Production host: Methylophaga aminisulfidivorans MP (bacteria)
References: UniProt: A3FJ51, methanol dehydrogenase (cytochrome c)
#3: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H6N2O8
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 977 / 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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate pH 6.5, 0.2M magnesium acetate tetrahydrate, 10%(v/v) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2009
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 140904 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 24.55
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.827 / Num. unique obs: 6897 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W6S

1w6s


Resolution: 1.701→34.724 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1814 7071 5.02 %
Rwork0.1511 --
obs0.1526 140904 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.701→34.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10376 0 50 977 11403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01310763
X-RAY DIFFRACTIONf_angle_d1.11214579
X-RAY DIFFRACTIONf_dihedral_angle_d13.2363860
X-RAY DIFFRACTIONf_chiral_restr0.0441454
X-RAY DIFFRACTIONf_plane_restr0.0061900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7007-1.72010.24792310.20064250X-RAY DIFFRACTION95
1.7201-1.74030.23282390.19774408X-RAY DIFFRACTION99
1.7403-1.76150.24112240.18424451X-RAY DIFFRACTION100
1.7615-1.78380.20892230.17324462X-RAY DIFFRACTION99
1.7838-1.80730.20942350.16894410X-RAY DIFFRACTION99
1.8073-1.83210.1992300.16724447X-RAY DIFFRACTION99
1.8321-1.85820.23432390.16754449X-RAY DIFFRACTION100
1.8582-1.8860.22222200.16144458X-RAY DIFFRACTION99
1.886-1.91540.18632310.1614457X-RAY DIFFRACTION100
1.9154-1.94680.19362470.15444437X-RAY DIFFRACTION99
1.9468-1.98040.18932340.15254468X-RAY DIFFRACTION100
1.9804-2.01640.18212340.15294454X-RAY DIFFRACTION100
2.0164-2.05520.18852360.15334437X-RAY DIFFRACTION100
2.0552-2.09710.19242310.15524477X-RAY DIFFRACTION100
2.0971-2.14270.1922170.15374487X-RAY DIFFRACTION100
2.1427-2.19260.18672330.1524483X-RAY DIFFRACTION100
2.1926-2.24740.18682340.14774440X-RAY DIFFRACTION100
2.2474-2.30810.19352670.14934465X-RAY DIFFRACTION100
2.3081-2.3760.18132350.15544482X-RAY DIFFRACTION100
2.376-2.45270.19392170.15534479X-RAY DIFFRACTION100
2.4527-2.54040.19352510.15914476X-RAY DIFFRACTION100
2.5404-2.6420.20332580.16314454X-RAY DIFFRACTION100
2.642-2.76220.1982250.1584499X-RAY DIFFRACTION100
2.7622-2.90780.19442000.16244531X-RAY DIFFRACTION100
2.9078-3.08990.2012180.174489X-RAY DIFFRACTION100
3.0899-3.32830.18712720.15864445X-RAY DIFFRACTION100
3.3283-3.66290.17352490.14744489X-RAY DIFFRACTION100
3.6629-4.19210.14222560.13084472X-RAY DIFFRACTION100
4.1921-5.27860.12392350.11254520X-RAY DIFFRACTION99
5.2786-34.73150.15472500.13184557X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 8.8433 Å / Origin y: -1.0738 Å / Origin z: 27.8722 Å
111213212223313233
T0.1116 Å2-0.0211 Å2-0.0163 Å2-0.0924 Å2-0.009 Å2--0.1084 Å2
L0.3224 °2-0.1575 °2-0.218 °2-0.2264 °20.1615 °2--0.3357 °2
S0.0252 Å °-0.0351 Å °-0.0007 Å °-0.0259 Å °-0.0274 Å °0.0135 Å °-0.0115 Å °-0.0069 Å °0.0016 Å °
Refinement TLS groupSelection details: all

+
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