[English] 日本語
Yorodumi
- PDB-7o6z: Structure of a neodymium-containing, XoxF1-type methanol dehydrogenase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o6z
TitleStructure of a neodymium-containing, XoxF1-type methanol dehydrogenase
ComponentsMethanol dehydrogenase (Cytochrome c) subunit 1
KeywordsOXIDOREDUCTASE / methanol dehydrogenase / neodymium / lanthanide / XoxF1
Function / homologyMETHANOL / : / PYRROLOQUINOLINE QUINONE
Function and homology information
Biological speciesMethylacidimicrobium sp. AP8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSchmitz, R. / Dietl, A. / Op den Camp, H. / Barends, T.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)VOLCANO 669371European Union
CitationJournal: Mbio / Year: 2021
Title: Neodymium as Metal Cofactor for Biological Methanol Oxidation: Structure and Kinetics of an XoxF1-Type Methanol Dehydrogenase.
Authors: Schmitz, R.A. / Picone, N. / Singer, H. / Dietl, A. / Seifert, K.A. / Pol, A. / Jetten, M.S.M. / Barends, T.R.M. / Daumann, L.J. / Op den Camp, H.J.M.
History
DepositionApr 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 17, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methanol dehydrogenase (Cytochrome c) subunit 1
B: Methanol dehydrogenase (Cytochrome c) subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,5677
Polymers136,8842
Non-polymers6835
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-18 kcal/mol
Surface area34490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.870, 70.180, 97.230
Angle α, β, γ (deg.)90.000, 91.394, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Methanol dehydrogenase (Cytochrome c) subunit 1 / XoxF1-type methanol dehydrogenase


Mass: 68442.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylacidimicrobium sp. AP8 (bacteria) / References: methanol dehydrogenase (cytochrome c)
#2: Chemical ChemComp-ND / Neodymium Ion


Mass: 144.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Nd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H6N2O8 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.01 M nickel chloride, 20% (w/v) PEG 2000 monomethyl ether, and 0.1 M Tris/HCl pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99985 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 2.3→48.6 Å / Num. obs: 51250 / % possible obs: 94.8 % / Redundancy: 2 % / Biso Wilson estimate: 42.79 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.4
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.787 / Num. unique obs: 3810 / CC1/2: 0.618 / % possible all: 96.1

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MAE

4mae


Resolution: 2.3→48.6 Å / SU ML: 0.3616 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.6628
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2515 1958 3.83 %
Rwork0.1948 49225 -
obs0.1969 51183 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.55 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9188 0 30 318 9536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00539504
X-RAY DIFFRACTIONf_angle_d1.14112942
X-RAY DIFFRACTIONf_chiral_restr0.06591326
X-RAY DIFFRACTIONf_plane_restr0.00842860
X-RAY DIFFRACTIONf_dihedral_angle_d11.29731284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.43341500.38123514X-RAY DIFFRACTION95.79
2.36-2.420.37951380.35233549X-RAY DIFFRACTION96.07
2.42-2.490.3931210.31283593X-RAY DIFFRACTION96.04
2.49-2.570.36611540.30033477X-RAY DIFFRACTION95.73
2.57-2.660.31711380.27723543X-RAY DIFFRACTION95.39
2.66-2.770.30381460.23853444X-RAY DIFFRACTION93.59
2.77-2.90.26131280.23123557X-RAY DIFFRACTION95.96
2.9-3.050.29061450.22563546X-RAY DIFFRACTION95.7
3.05-3.240.26721280.21033553X-RAY DIFFRACTION95.51
3.24-3.490.27361550.18833506X-RAY DIFFRACTION95.09
3.49-3.840.27071290.19743508X-RAY DIFFRACTION94
3.84-4.40.22311460.14343493X-RAY DIFFRACTION93.6
4.4-5.540.15361370.12963446X-RAY DIFFRACTION92.37
5.54-48.60.19161430.14833496X-RAY DIFFRACTION90.91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.110481308730.282114975612-0.4978440654560.828746910363-0.200069922560.9597473195480.0449200803706-0.2081651300270.09810874812170.09442059803620.03136354537570.0223437093447-0.1376310597140.0950664206534-0.0764506095240.3413063249240.02630432537350.01446700256430.361673484022-0.03136458567150.344422202178-39.2209392191-7.314931987623.7953645836
21.67640237973-0.152610177413-0.2716670252610.407565026927-0.1070144545310.813273217368-0.0784929570309-0.245608755709-0.2879565373460.08914043496390.08147363122210.1096494639480.0769638413038-0.182112177584-0.006933306929830.371920555720.02816067632150.02871757446440.3860582103380.05946272110090.414999996877-80.3494567309-34.169484561526.6406039192
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 32 - 619 / Label seq-ID: 1 - 590

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 32 through 801)AA
22(chain 'B' and resid 32 through 801)BD

+
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