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- PDB-5laa: X-RAY STRUCTURE OF THE METHYLTRANSFERASE SUBUNIT A FROM METHANOTH... -

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Basic information

Entry
Database: PDB / ID: 5laa
TitleX-RAY STRUCTURE OF THE METHYLTRANSFERASE SUBUNIT A FROM METHANOTHERMUS FERVIDUS IN COMPLEX WITH COBALAMIN
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 activity / tetrahydromethanopterin S-methyltransferase / methanogenesis, from carbon dioxide / sodium ion transport / cobalt ion binding / one-carbon metabolic process / methylation / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Tetrahydromethanopterin S-methyltransferase subunit A, MtrA / Methyltransferase MtrA/MtxA / Tetrahydromethanopterin S-methyltransferase, subunit A
Similarity search - Domain/homology
COBALAMIN / Tetrahydromethanopterin S-methyltransferase subunit A
Similarity search - Component
Biological speciesMethanothermus fervidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 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 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Experimental preparation / Source and taxonomy
Category: diffrn_source / entity_src_gen / exptl_crystal_grow
Item: _diffrn_source.pdbx_wavelength_list / _entity_src_gen.pdbx_gene_src_atcc ..._diffrn_source.pdbx_wavelength_list / _entity_src_gen.pdbx_gene_src_atcc / _entity_src_gen.pdbx_gene_src_cell / _entity_src_gen.pdbx_gene_src_cell_line / _entity_src_gen.pdbx_gene_src_organ / _exptl_crystal_grow.pdbx_pH_range
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Tetrahydromethanopterin S-methyltransferase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8226
Polymers54,8313
Non-polymers3,9913
Water00
1
A: Tetrahydromethanopterin S-methyltransferase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5132
Polymers18,1831
Non-polymers1,3301
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tetrahydromethanopterin S-methyltransferase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5132
Polymers18,1831
Non-polymers1,3301
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tetrahydromethanopterin S-methyltransferase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7952
Polymers18,4651
Non-polymers1,3301
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.604, 100.604, 262.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLUGLUAA2 - 1592 - 159
21VALVALGLUGLUBB2 - 1592 - 159
12METMETPHEPHEAA1 - 1581 - 158
22METMETPHEPHECC1 - 1584 - 161
13VALVALPHEPHEBB2 - 1582 - 158
23VALVALPHEPHECC2 - 1585 - 161

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 18182.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Obtained from gene synthesis
Source: (gene. exp.) Methanothermus fervidus (strain ATCC 43054 / DSM 2088 / JCM 10308 / V24 S) (archaea)
Strain: ATCC 43054 / DSM 2088 / JCM 10308 / V24 S / Tissue: / / Gene: mtrA, Mfer_0072 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E3GWY7, tetrahydromethanopterin S-methyltransferase
#2: Protein Tetrahydromethanopterin S-methyltransferase subunit A / N5-methyltetrahydromethanopterin--coenzyme M methyltransferase subunit A


Mass: 18465.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Obtained from gene synthesis
Source: (gene. exp.) Methanothermus fervidus (strain ATCC 43054 / DSM 2088 / JCM 10308 / V24 S) (archaea)
Strain: ATCC 43054 / DSM 2088 / JCM 10308 / V24 S / Tissue: / / Gene: mtrA, Mfer_0072 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E3GWY7, tetrahydromethanopterin S-methyltransferase
#3: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C62H89CoN13O14P

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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: 3.05 Å3/Da / Density % sol: 59.7 %
Description: About 100 microns cube, pink colour and brick shape
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein concentration 20 mg/mL complexed with hydroxy-cobalamin. A pink brick shape crystal appeared in 26% PEG 3000, 100 mM Na citrate pH 5.5.
Temp details: The unique crystal which appeared after 1 year was obtained at room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.602 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.602 Å / Relative weight: 1
ReflectionResolution: 3→131.35 Å / Num. obs: 13764 / % possible obs: 98.5 % / Redundancy: 17.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.224 / Rsym value: 0.074 / Net I/σ(I): 8.6
Reflection shellResolution: 3→3.18 Å / Redundancy: 11.9 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 2.5 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3→131.35 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 50.138 / SU ML: 0.408 / Cross valid method: FREE R-VALUE / ESU R Free: 0.427
RfactorNum. reflection% reflectionSelection details
Rfree0.25424 681 5 %RANDOM
Rwork0.20838 ---
obs0.21057 13073 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 86.158 Å2
Baniso -1Baniso -2Baniso -3
1-4.35 Å2-0 Å20 Å2
2--4.35 Å20 Å2
3----8.69 Å2
Refinement stepCycle: 1 / Resolution: 3→131.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 273 0 3917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194005
X-RAY DIFFRACTIONr_bond_other_d0.0060.0193935
X-RAY DIFFRACTIONr_angle_refined_deg2.3022.0735504
X-RAY DIFFRACTIONr_angle_other_deg1.57839123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4065477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38327.07157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25115679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.208159
X-RAY DIFFRACTIONr_chiral_restr0.2110.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024419
X-RAY DIFFRACTIONr_gen_planes_other0.0040.019769
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8764.6511917
X-RAY DIFFRACTIONr_mcbond_other1.8744.6511916
X-RAY DIFFRACTIONr_mcangle_it3.3066.9632391
X-RAY DIFFRACTIONr_mcangle_other3.3066.9642392
X-RAY DIFFRACTIONr_scbond_it1.9915.2932086
X-RAY DIFFRACTIONr_scbond_other1.9915.2942087
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4327.8993113
X-RAY DIFFRACTIONr_long_range_B_refined5.78638.3774158
X-RAY DIFFRACTIONr_long_range_B_other5.78538.3844159
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A190220.11
12B190220.11
21A191820.1
22C191820.1
31B187140.11
32C187140.11
LS refinement shellResolution: 3.001→3.079 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 48 -
Rwork0.455 812 -
obs--85.66 %
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)
15.30480.81210.91463.25210.78564.320.1112-0.1748-0.23690.19920.027-0.0660.19010.0477-0.13820.49580.10430.02950.4303-0.00420.01716.025140.8163119.9428
23.01860.36630.31524.4476-0.91814.4053-0.1833-0.1051-0.325-0.03640.12680.25530.29640.01260.05650.40320.0360.07940.3912-0.00290.088-9.319425.253593.2091
31.97560.1308-0.46424.40341.3725.0707-0.12420.1509-0.021-0.2081-0.0235-0.31960.28650.32040.14780.46330.0210.07740.51360.04790.145321.644448.851481.1359
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 159
2X-RAY DIFFRACTION2B2 - 160
3X-RAY DIFFRACTION3C1 - 159

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