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- PDB-8ssc: Full-Length Methionine synthase from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 8ssc
TitleFull-Length Methionine synthase from Thermus thermophilus HB8
ComponentsMethionine synthase
KeywordsTRANSFERASE / Methyl transferase / cobalamin-dependent / cobalamin binding / one-carbon metabolism
Function / homology
Function and homology information


methionine synthase / methionine synthase activity / homocysteine metabolic process / cobalamin binding / tetrahydrofolate metabolic process / methylation / zinc ion binding / cytosol
Similarity search - Function
Vitamin B12-dependent methionine synthase, activation domain / Vitamin B12 dependent methionine synthase, activation domain / AdoMet activation domain profile. / Cobalamin-dependent methionine synthase / Methionine synthase, B12-binding domain / Vitamin B12-dependent methionine synthase, activation domain superfamily / B12-binding N-terminal domain profile. / B12 binding domain / Homocysteine-binding domain / Homocysteine-binding domain superfamily ...Vitamin B12-dependent methionine synthase, activation domain / Vitamin B12 dependent methionine synthase, activation domain / AdoMet activation domain profile. / Cobalamin-dependent methionine synthase / Methionine synthase, B12-binding domain / Vitamin B12-dependent methionine synthase, activation domain superfamily / B12-binding N-terminal domain profile. / B12 binding domain / Homocysteine-binding domain / Homocysteine-binding domain superfamily / Homocysteine S-methyltransferase / Homocysteine-binding domain profile. / : / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methionine synthase domain / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like
Similarity search - Domain/homology
: / Methionine synthase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsYamada, K. / Mendoza, J. / Koutmos, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1945174 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structure of full-length cobalamin-dependent methionine synthase and cofactor loading captured in crystallo.
Authors: Mendoza, J. / Purchal, M. / Yamada, K. / Koutmos, M.
History
DepositionMay 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,6034
Polymers127,3711
Non-polymers2313
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.804, 134.804, 174.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Methionine synthase / 5-methyltetrahydrofolate--homocysteine methyltransferase


Mass: 127371.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: ATCC 27634 / DSM 579 / HB8 / Gene: TTHA0618 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKM5, methionine synthase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
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: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M trimethylamine N-oxide, 0.1 M Tris-HCl, pH 8.5, 20% (w/v) Polyethylene glycol monomethylethe

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 10, 2013
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.75→106.64 Å / Num. obs: 42467 / % possible obs: 100 % / Redundancy: 15.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.049 / Rrim(I) all: 0.197 / Χ2: 0.99 / Net I/σ(I): 12.3 / Num. measured all: 669916
Reflection shellResolution: 2.75→2.85 Å / % possible obs: 100 % / Redundancy: 11.7 % / Rmerge(I) obs: 1.6 / Num. measured all: 51333 / Num. unique obs: 4373 / CC1/2: 0.672 / Rpim(I) all: 0.481 / Rrim(I) all: 1.673 / Χ2: 1.03 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→106.64 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.905 / SU B: 13.248 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.828 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25258 2154 5.1 %RANDOM
Rwork0.20188 ---
obs0.20444 40236 99.98 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 79.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å20 Å2
2--0.15 Å20 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 2.75→106.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8754 0 11 225 8990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0128971
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168704
X-RAY DIFFRACTIONr_angle_refined_deg1.271.64812138
X-RAY DIFFRACTIONr_angle_other_deg0.4021.56520005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45351124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.243581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.683101530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0550.21339
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210602
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022054
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_it7.7257.8884493
X-RAY DIFFRACTIONr_mcbond_other7.7237.8884493
X-RAY DIFFRACTIONr_mcangle_it11.00214.215612
X-RAY DIFFRACTIONr_mcangle_other11.00114.2115613
X-RAY DIFFRACTIONr_scbond_it7.8148.4414478
X-RAY DIFFRACTIONr_scbond_other7.768.4324470
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.49515.2376513
X-RAY DIFFRACTIONr_long_range_B_refined15.98293.2138902
X-RAY DIFFRACTIONr_long_range_B_other15.98593.2738805
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.752→2.824 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 134 -
Rwork0.294 2937 -
obs--99.9 %

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