[English] 日本語
Yorodumi
- PDB-6tm3: Structure of methylene-tetrahydromethanopterin dehydrogenase from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tm3
TitleStructure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in a close conformation containing NADP+ and methylene-H4MPT
ComponentsBifunctional protein MdtA
KeywordsOXIDOREDUCTASE / One-carbon metabolism / Enzyme catalysis / Dehydrogenase / Conformational changes / Methylotrophy
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor / methylenetetrahydrofolate dehydrogenase (NADP+) / methylenetetrahydrofolate dehydrogenase (NADP+) activity / formaldehyde catabolic process / one-carbon metabolic process / cytoplasm
Similarity search - Function
Methylene-tetrahydromethanopterin dehydrogenase, N-terminal domain / Methylene-tetrahydromethanopterin dehydrogenase, N-terminal / Methylene tetrahydromethanopterin dehydrogenase, NADP-binding domain / Methylene-tetrahydromethanopterin dehydrogenase, N-terminal domain superfamily / Methylene-tetrahydromethanopterin dehydrogenase, N-terminal / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Bifunctional protein MdtA
Similarity search - Component
Biological speciesMethylorubrum extorquens AM1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsWagner, T. / Huang, G. / Demmer, U. / Warkentin, E. / Ermler, U. / Shima, S.
Funding support Germany, China, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)Iron sulfur for life SH87/1-1 Germany
Ministry of Education (MoE, China)China Scholarship Council China
CitationJournal: J.Mol.Biol. / Year: 2020
Title: The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase.
Authors: Huang, G. / Wagner, T. / Demmer, U. / Warkentin, E. / Ermler, U. / Shima, S.
History
DepositionDec 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: 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
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bifunctional protein MdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,02020
Polymers31,5131
Non-polymers2,50719
Water9,026501
1
A: Bifunctional protein MdtA
hetero molecules

A: Bifunctional protein MdtA
hetero molecules

A: Bifunctional protein MdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,05960
Polymers94,5383
Non-polymers7,52157
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area20300 Å2
ΔGint26 kcal/mol
Surface area30250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.754, 125.754, 125.754
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-696-

HOH

21A-795-

HOH

31A-823-

HOH

41A-871-

HOH

51A-891-

HOH

61A-927-

HOH

71A-962-

HOH

81A-978-

HOH

91A-979-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Bifunctional protein MdtA


Mass: 31512.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens AM1 (bacteria)
Gene: mtdA, MexAM1_META1p1728 / Plasmid: pET-24b(+)
Details (production host): The synthesized DNA fragment was inserted into the expression vector pET-24b (+) at the NdeI and SalI restriction-enzyme digestion-sites.
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P55818, Oxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor, methylenetetrahydrofolate dehydrogenase (NADP+)

-
Non-polymers , 6 types, 520 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-H4M / 5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN


Mass: 788.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H45N6O16P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: The crystallized sample was 25 mg/ml MtdA supplemented with 2.5 mM methenyl-H4MPT, 2 mM NADPH in 25 mM Tris/HCl pH 7.5, 150 mM NaCl, 5% glycerol and 2 mM dithiothreitol. 0.7 ul protein ...Details: The crystallized sample was 25 mg/ml MtdA supplemented with 2.5 mM methenyl-H4MPT, 2 mM NADPH in 25 mM Tris/HCl pH 7.5, 150 mM NaCl, 5% glycerol and 2 mM dithiothreitol. 0.7 ul protein sample was mixed with 0.7 ul of the reservoir solution containing 30% w/v polyethylene glycol monomethyl ether 5000, 100 mM Tris pH 8.0 and 200 mM lithium sulfate.
PH range: / / Temp details: /

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.08→88.922 Å / Num. all: 143688 / Num. obs: 143688 / % possible obs: 99.6 % / Redundancy: 10 % / Rpim(I) all: 0.016 / Rrim(I) all: 0.051 / Rsym value: 0.049 / Net I/av σ(I): 10.3 / Net I/σ(I): 25.1 / Num. measured all: 1439110
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.08-1.144.71.4030.695042202230.7051.5781.4031.197.6
1.14-1.219.90.8680.9194538196970.2890.9150.8682.9100
1.21-1.2910.70.5651.4198949185430.180.5930.5655100
1.29-1.3911.70.3582.2202723173040.1090.3740.3588.2100
1.39-1.5311.40.1864.2181856159610.0580.1950.18614.8100
1.53-1.7111.90.0968.2172492145100.0290.10.09627.2100
1.71-1.9711.20.04915.3143991128630.0150.0520.04945.5100
1.97-2.4110.90.0323.5119084109720.0090.0310.0371.1100
2.41-3.429.80.02325.98432686140.0070.0240.02388.9100
3.42-41.9189.20.02294610950010.0070.0210.02105.199.9

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LU9

1lu9


Resolution: 1.08→41.918 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 13.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.127 7168 5 %
Rwork0.1128 136110 -
obs0.1135 143278 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.59 Å2 / Biso mean: 18.0707 Å2 / Biso min: 9.27 Å2
Refinement stepCycle: final / Resolution: 1.08→41.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 144 501 2743
Biso mean--23.52 32.59 -
Num. residues----289
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.08-1.09230.42742230.392394888
1.0923-1.10510.33592440.3359426295
1.1051-1.11860.33912200.3035446299
1.1186-1.13280.29322430.27244539100
1.1328-1.14770.26252490.25354440100
1.1477-1.16340.23812650.22884483100
1.1634-1.180.22482160.20114517100
1.18-1.19760.20622340.18774531100
1.1976-1.21630.18472310.17444542100
1.2163-1.23630.17552350.16034484100
1.2363-1.25760.16962540.14824517100
1.2576-1.28050.1542350.14054519100
1.2805-1.30510.15442490.12374500100
1.3051-1.33170.12552110.11524546100
1.3317-1.36070.12682390.10734534100
1.3607-1.39240.13092200.10444554100
1.3924-1.42720.12862410.09534557100
1.4272-1.46580.11232350.08814558100
1.4658-1.50890.10282240.08154553100
1.5089-1.55760.09422340.07354545100
1.5576-1.61330.09852250.07254576100
1.6133-1.67790.08572410.07434592100
1.6779-1.75420.08612300.07634572100
1.7542-1.84670.09932620.07944578100
1.8467-1.96240.09512660.0844561100
1.9624-2.1140.1112190.08824648100
2.114-2.32670.09512140.08814666100
2.3267-2.66330.10642780.09574630100
2.6633-3.35530.1132600.10854735100
3.3553-41.9180.13812710.12634961100

+
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