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- PDB-6tm3: Structure of methylene-tetrahydromethanopterin dehydrogenase from... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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+)

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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

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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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: /

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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

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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

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