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- PDB-5l8x: X-RAY STRUCTURE OF APO METHANOCALDOCOCCUS JANNASCHII METHYLTRANSF... -

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Basic information

Entry
Database: PDB / ID: 5l8x
TitleX-RAY STRUCTURE OF APO METHANOCALDOCOCCUS JANNASCHII METHYLTRANSFERASE SUBUNIT A AT 1.85 ANGSTROM
Components(Tetrahydromethanopterin S-methyltransferase subunit A) x 2
KeywordsTRANSFERASE / Methanogenesis / Motor pump / Membrane protein / Methyltransferase / Cobalamin / Vitamin B12 / CoenzymeM / Rossmann fold / Hyperthermophile / Marine organism
Function / homology
Function and homology information


tetrahydromethanopterin S-methyltransferase / tetrahydromethanopterin S-methyltransferase activity / methanogenesis, from carbon dioxide / cobalt ion binding / one-carbon metabolic process / methylation / plasma membrane
Similarity search - Function
Tetrahydromethanopterin S-methyltransferase subunit A, MtrA / Methyltransferase MtrA/MtxA / Tetrahydromethanopterin S-methyltransferase, subunit A
Similarity search - Domain/homology
(2S)-2-hydroxybutanedioic acid / D-MALATE / Tetrahydromethanopterin S-methyltransferase subunit A
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWagner, T. / Ermler, U. / Shima, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and technology agency (JST)PRESTO Japan
CitationJournal: Sci Rep / Year: 2016
Title: MtrA of the sodium ion pumping methyltransferase binds cobalamin in a unique mode.
Authors: Wagner, T. / Ermler, U. / Shima, S.
History
DepositionJun 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetrahydromethanopterin S-methyltransferase subunit A
B: Tetrahydromethanopterin S-methyltransferase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1274
Polymers36,8592
Non-polymers2682
Water1,820101
1
A: Tetrahydromethanopterin S-methyltransferase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5352
Polymers18,4011
Non-polymers1341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tetrahydromethanopterin S-methyltransferase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5922
Polymers18,4581
Non-polymers1341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.690, 37.030, 65.160
Angle α, β, γ (deg.)90.00, 91.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tetrahydromethanopterin S-methyltransferase subunit A / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit A


Mass: 18400.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The HexaHistidine tagged in the N-terminus has been partially cleaved during limited proteolysis as the C-terminus. The original construct corresponds to MtrA 1-220.
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Gene: mtrA, MJ0851 / Plasmid: pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q58261, tetrahydromethanopterin S-methyltransferase
#2: Protein Tetrahydromethanopterin S-methyltransferase subunit A / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit A


Mass: 18457.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The HexaHistidine tagged in the N-terminus has been partially cleaved during limited proteolysis as the C-terminus. The original construct corresponds to MtrA 1-220.
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Gene: mtrA, MJ0851 / Plasmid: pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q58261, tetrahydromethanopterin S-methyltransferase
#3: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.42 %
Description: Tiny needles can have a maximum length of about 200 microns
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 50 mg/ml protein after 2 months incubation, transparent needle-type crystals were reproducibly obtained in 2.2 M D/L-malate pH 7.6, 100 mM Tris-HCl pH 8.0
Temp details: Best crystals appeared at 281.15 K but smaller needles can appear at higher temperature too

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→45.11 Å / Num. obs: 25433 / % possible obs: 95.4 % / Redundancy: 2.3 % / CC1/2: 0.983 / Rmerge(I) obs: 0.123 / Rsym value: 0.093 / Net I/σ(I): 6.1
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREP11.0.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MtrA cytoplasmic Methanothermus fervidus

Resolution: 1.85→45.108 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.92
RfactorNum. reflection% reflection
Rfree0.2371 1280 5.03 %
Rwork0.1869 --
obs0.1894 25433 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.6 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2569 0 18 101 2688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092631
X-RAY DIFFRACTIONf_angle_d1.1973565
X-RAY DIFFRACTIONf_dihedral_angle_d13.869965
X-RAY DIFFRACTIONf_chiral_restr0.054397
X-RAY DIFFRACTIONf_plane_restr0.006479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.92410.30711390.25932675X-RAY DIFFRACTION96
1.9241-2.01170.28481350.24912674X-RAY DIFFRACTION96
2.0117-2.11770.29351470.21622638X-RAY DIFFRACTION96
2.1177-2.25040.2621450.20972646X-RAY DIFFRACTION94
2.2504-2.42410.26111500.20382669X-RAY DIFFRACTION95
2.4241-2.66810.2351330.19912713X-RAY DIFFRACTION96
2.6681-3.05410.27731480.19112675X-RAY DIFFRACTION95
3.0541-3.84750.21481370.16882709X-RAY DIFFRACTION95
3.8475-45.12130.18151460.14912754X-RAY DIFFRACTION94
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)
11.24420.73820.85171.65691.47913.56740.2179-0.33750.00590.3771-0.00930.13980.1346-0.633-0.02210.18410.01920.02090.22430.01730.1572-23.44453.864326.0585
21.9622-0.0388-0.050.8663-0.58282.1058-0.1016-0.21-0.28190.03880.0848-0.00640.2438-0.07040.02670.1112-0.0124-0.00420.09880.03550.1469-15.2805-2.669221.6822
32.95330.5302-0.40661.1878-0.44664.18970.0686-0.0686-0.24760.08130.2176-0.2030.28160.4287-0.30870.10470.0041-0.03440.1611-0.00350.1785-3.0086-0.284115.0558
42.0779-0.0701-0.20273.36250.96761.37350.04460.57250.3636-0.29130.0576-0.1408-0.18410.1043-0.07740.1536-0.05070.00350.16370.06340.1582-6.21037.90647.8497
52.69910.22340.13012.21440.1872.39190.0191-0.0230.63690.0876-0.0144-0.3214-0.54970.27340.13120.2033-0.06910.01670.08730.00760.2133-12.08413.107219.1052
62.6096-0.8026-1.30611.9847-0.34162.7102-0.2246-0.576-0.33990.15890.0462-0.23060.26310.56950.16710.15860.0387-0.01980.27580.06960.2097-7.2177-4.905129.9009
71.9740.1097-0.54932.34680.75922.91470.2342-0.18460.1398-0.0384-0.02250.055-0.5899-0.5306-0.21460.15950.01690.00430.14640.00110.1791-20.173710.806321.0175
82.44810.2225-0.85810.82720.43750.6145-0.16610.4783-0.11920.04760.11970.50130.0872-0.4230.03340.1806-0.02610.0640.39440.14990.2727-25.423-4.8601-22.0694
90.82540.2541-1.47661.3405-0.66913.3341-0.12360.3047-0.1561-0.16960.17730.10110.87-0.61530.00050.2492-0.0967-0.03030.18990.02570.1427-19.4655-12.2225-14.6836
103.2319-0.5565-0.1223.444-0.22623.7752-0.0212-0.18830.1499-0.02550.1524-0.1997-0.12440.68-0.09930.1642-0.04710.01690.1987-0.03690.125-10.7569-5.1193-2.892
111.14570.0003-1.00192.4171-1.11283.6523-0.02480.30490.10090.21150.30460.18860.0433-0.9072-0.08430.2027-0.01930.01220.2780.06790.1357-24.1235-6.6185-10.9966
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 79 )
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 97 )
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 119 )
5X-RAY DIFFRACTION5chain 'A' and (resid 120 through 129 )
6X-RAY DIFFRACTION6chain 'A' and (resid 130 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 170 )
8X-RAY DIFFRACTION8chain 'B' and (resid -2 through 17 )
9X-RAY DIFFRACTION9chain 'B' and (resid 18 through 79 )
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 119 )
11X-RAY DIFFRACTION11chain 'B' and (resid 120 through 169 )

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