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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tlk
TitleStructure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in an open 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
FORMIC ACID / 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: 1.8 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 FoundationIron sulfur for life SH87/1-1 Germany
Ministry of Education (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 2, 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.ptnr3_auth_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_symmetry / _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_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bifunctional protein MdtA
B: Bifunctional protein MdtA
C: Bifunctional protein MdtA
D: Bifunctional protein MdtA
E: Bifunctional protein MdtA
F: Bifunctional protein MdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,32535
Polymers189,0766
Non-polymers7,24829
Water37,7052093
1
A: Bifunctional protein MdtA
B: Bifunctional protein MdtA
C: Bifunctional protein MdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,71414
Polymers94,5383
Non-polymers4,17611
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-28 kcal/mol
Surface area32470 Å2
MethodPISA
2
D: Bifunctional protein MdtA
E: Bifunctional protein MdtA
F: Bifunctional protein MdtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,61121
Polymers94,5383
Non-polymers3,07318
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint-38 kcal/mol
Surface area32410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.923, 149.267, 78.559
Angle α, β, γ (deg.)90.000, 93.640, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Bifunctional protein MdtA


Mass: 31512.734 Da / Num. of mol.: 6
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 , 7 types, 2122 molecules

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


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-H4M / 5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN


Mass: 788.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H45N6O16P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2093 / 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: 2.52 Å3/Da / Density % sol: 51.14 % / Description: Thick plate.
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The protein at 25 mg/ml was in 25 mM tris(hydroxymethyl)aminomethane (Tris)/HCl buffer pH 7.5 containing 150 mM NaCl, 5% glycerol and 2 mM dithiothreitol, supplemented with 2.5 mM methenyl- ...Details: The protein at 25 mg/ml was in 25 mM tris(hydroxymethyl)aminomethane (Tris)/HCl buffer pH 7.5 containing 150 mM NaCl, 5% glycerol and 2 mM dithiothreitol, supplemented with 2.5 mM methenyl-H4MPT and 2 mM NADP. The crystallization solution was 20% w/v polyethylene glycol 3350 and 200 mM magnesium formate. The crystallization drop contained 0.7 ul of protein solution and 0.7 ul crystallization solution
PH range: / / Temp details: /

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97992 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97992 Å / Relative weight: 1
ReflectionResolution: 1.8→78.401 Å / Num. obs: 161189 / % possible obs: 98.9 % / Redundancy: 3 % / Biso Wilson estimate: 28.48 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.044 / Rrim(I) all: 0.08 / Rsym value: 0.066 / Net I/av σ(I): 10.5 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.8-1.931.0320.8236240.5430.691.2471.03299.5
1.9-2.0130.5111.5224230.3420.6180.51199.5
2.01-2.1530.3122.5209490.2090.3770.31299.5
2.15-2.3230.1894.1196120.1260.2280.18999.4
2.32-2.5530.1246.1180080.0830.150.12499.3
2.55-2.8530.07410.2162490.0490.0890.07499
2.85-3.2930.04217.3142490.0280.0510.04298.5
3.29-4.0230.02823.8119430.0180.0330.02897.7
4.02-5.6930.02227.291680.0150.0270.02296.6
5.69-43.3163.10.0227.149640.0130.0240.0294.7

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LU9

1lu9


Resolution: 1.8→26.35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.126 / SU Rfree Blow DPI: 0.116 / SU Rfree Cruickshank DPI: 0.111
RfactorNum. reflection% reflectionSelection details
Rfree0.201 7909 4.91 %RANDOM
Rwork0.166 ---
obs0.167 161135 98.8 %-
Displacement parametersBiso max: 136.77 Å2 / Biso mean: 36.17 Å2 / Biso min: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.0754 Å20 Å25.0536 Å2
2---0.6214 Å20 Å2
3----0.454 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.8→26.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12548 0 489 2093 15130
Biso mean--41.63 42.77 -
Num. residues----1729
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5875SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4192HARMONIC5
X-RAY DIFFRACTIONt_it26189HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1723SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact28217SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d26189HARMONIC50.009
X-RAY DIFFRACTIONt_angle_deg47297HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion13.72
LS refinement shellResolution: 1.8→1.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2672 580 4.86 %
Rwork0.2288 11364 -
all0.2306 11944 -
obs--99.44 %
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)
11.08220.86390.24890.8134-0.03970.3720.0135-0.0067-0.03970.0394-0.0519-0.0079-0.09320.00730.0383-0.0294-0.01890.0047-0.05640.0093-0.003-10.228417.709359.5854
21.2370.5301-0.78170.4241-0.04630.2669-0.0876-0.0079-0.04810.0152-0.0013-0.1026-0.0057-0.03260.0889-0.0757-0.0168-0.0470.01030.0382-0.0225-48.9332-5.643754.2022
30.2995-0.35260.62820.3938-0.62891.31310.00110.10170.173-0.03920.08180.0240.05570.035-0.0829-0.0918-0.0672-0.01010.00760.13060.0456-33.338521.415820.4543
40.6339-0.14130.31710.47170.22751.50210.0044-0.1438-0.12330.048-0.00430.04260.18780.021-0.0002-0.0307-0.01940.0145-0.03310.0627-0.0543-13.4285-23.997458.8399
51.09830.71450.26650.5536-0.14120.61960.03110.06870.0152-0.0880.08530.03770.1717-0.0772-0.11640.0284-0.0189-0.0535-0.04990.0143-0.0373-33.9984-27.108317.5657
60.44780.182-0.02860.4778-0.60630.9001-0.020.02440.05180.0476-0.06670.0103-0.08030.22020.0867-0.0177-0.042-0.01190.00570.0135-0.05621.8783-0.013423.0665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 456
2X-RAY DIFFRACTION2{ B|* }B2 - 456
3X-RAY DIFFRACTION3{ C|* }C2 - 456
4X-RAY DIFFRACTION4{ D|* }D2 - 456
5X-RAY DIFFRACTION5{ E|* }E2 - 456
6X-RAY DIFFRACTION6{ F|* }F2 - 456

+
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