[English] 日本語
Yorodumi
- PDB-1u6i: The Structure of native coenzyme F420-dependent methylenetetrahyd... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u6i
TitleThe Structure of native coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase at 2.2A resolution
ComponentsF420-dependent methylenetetrahydromethanopterin dehydrogenase
KeywordsOXIDOREDUCTASE / MONOMER: ALPHA/BETA DOMAIN / HELIX BUNDLE / TRIMER OF DIMERS
Function / homology
Function and homology information


methylenetetrahydromethanopterin dehydrogenase / methylenetetrahydromethanopterin dehydrogenase activity / methanogenesis, from carbon dioxide / ferredoxin hydrogenase activity / one-carbon metabolic process
Similarity search - Function
F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) / Helix Hairpins - #120 / F420-dependent methylenetetrahydromethanopterin dehydrogenase / F420-dependent methylenetetrahydromethanopterin dehydrogenase superfamily / methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase / Helix Hairpins / Helix non-globular / Special / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
F420-dependent methylenetetrahydromethanopterin dehydrogenase
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsWarkentin, E. / Hagemeier, C.H. / Shima, S. / Thauer, R.K. / Ermler, U.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: The structure of F420-dependent methylenetetrahydromethanopterin dehydrogenase: a crystallographic 'superstructure' of the selenomethionine-labelled protein crystal structure.
Authors: Warkentin, E. / Hagemeier, C.H. / Shima, S. / Thauer, R.K. / Ermler, U.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: a methanogenic enzyme with an unusual quarternary structure.
Authors: Hagemeier, C.H. / Shima, S. / Thauer, R.K. / Bourenkov, G. / Bartunik, H.D. / Ermler, U.
History
DepositionJul 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _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: F420-dependent methylenetetrahydromethanopterin dehydrogenase
B: F420-dependent methylenetetrahydromethanopterin dehydrogenase
C: F420-dependent methylenetetrahydromethanopterin dehydrogenase
D: F420-dependent methylenetetrahydromethanopterin dehydrogenase
E: F420-dependent methylenetetrahydromethanopterin dehydrogenase
F: F420-dependent methylenetetrahydromethanopterin dehydrogenase
G: F420-dependent methylenetetrahydromethanopterin dehydrogenase
H: F420-dependent methylenetetrahydromethanopterin dehydrogenase
I: F420-dependent methylenetetrahydromethanopterin dehydrogenase
J: F420-dependent methylenetetrahydromethanopterin dehydrogenase
K: F420-dependent methylenetetrahydromethanopterin dehydrogenase
L: F420-dependent methylenetetrahydromethanopterin dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)377,18520
Polymers376,99112
Non-polymers1948
Water11,998666
1
A: F420-dependent methylenetetrahydromethanopterin dehydrogenase
B: F420-dependent methylenetetrahydromethanopterin dehydrogenase
C: F420-dependent methylenetetrahydromethanopterin dehydrogenase
D: F420-dependent methylenetetrahydromethanopterin dehydrogenase
E: F420-dependent methylenetetrahydromethanopterin dehydrogenase
F: F420-dependent methylenetetrahydromethanopterin dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,59310
Polymers188,4956
Non-polymers974
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29690 Å2
ΔGint-198 kcal/mol
Surface area50390 Å2
MethodPISA
2
G: F420-dependent methylenetetrahydromethanopterin dehydrogenase
H: F420-dependent methylenetetrahydromethanopterin dehydrogenase
I: F420-dependent methylenetetrahydromethanopterin dehydrogenase
J: F420-dependent methylenetetrahydromethanopterin dehydrogenase
K: F420-dependent methylenetetrahydromethanopterin dehydrogenase
L: F420-dependent methylenetetrahydromethanopterin dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,59310
Polymers188,4956
Non-polymers974
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29620 Å2
ΔGint-193 kcal/mol
Surface area50490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.9, 118.9, 219.2
Angle α, β, γ (deg.)90., 90.01, 90.
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
F420-dependent methylenetetrahydromethanopterin dehydrogenase / MTD / Coenzyme F420 dependent N5 / N10- methylenetetrahydromethanopterin dehydrogenase


Mass: 31415.885 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: mtd / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P94951, EC: 1.5.99.9
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.6 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MOPS, KOH, MPD, PEG 400, Mg acetate, Na phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 2002
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 190905 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 1.86 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.141 / Rsym value: 0.064 / Net I/σ(I): 6.5
Reflection shellResolution: 2.2→2.4 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 4.4 / Num. unique all: 38875 / Rsym value: 0.129 / % possible all: 93.6

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
XDSdata scaling
CNSphasing
RefinementStarting model: Selenomethionine-labelled methylenetetrahydromethanopterin dehydrogenase (MTD), PDB-ID 1QV9

1qv9


Resolution: 2.2→19.35 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 9714980.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Description of the kMtd(Se) structure (PDB-ID 1QV9; space group C2221) in C2, a, subgroup of C2221
RfactorNum. reflection% reflectionSelection details
Rfree0.235 9126 4.7 %RANDOM WITH HEMIHEDRAL TWINNING
Rwork0.189 ---
obs-186249 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.3 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1-8.88 Å20 Å20 Å2
2---13.12 Å20 Å2
3---4.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26184 0 8 666 26858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.91
Refine LS restraints NCSNCS model details: THE MAIN-CHAIN ATOMS OF THE 2ND HEXAMER WERE STRONGLY TIED TO THE FIRST, THE SIDE-CHAIN ATOMS LESS TIGHT. IN ADDITION THE (PSEUDO) TWO-FOLD ALONG THE A AXIS WAS WEAKLY IMPOSED.
LS refinement shellResolution: 2.2→2.37 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 1625 4.2 %
Rwork0.267 33238 -
obs-34833 89.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

+
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