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- PDB-8ssd: Methionine synthase, C-terminal fragment, Cobalamin and Reactivat... -

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Basic information

Entry
Database: PDB / ID: 8ssd
TitleMethionine synthase, C-terminal fragment, Cobalamin and Reactivation Domains from Thermus thermophilus HB8
ComponentsMethionine synthase
KeywordsTRANSFERASE / Methyl transferase / cobalamin-dependent / methionine synthase / cobalamin binding / one-carbon metabolism
Function / homology
Function and homology information


pteridine-containing compound metabolic process / methionine synthase / methionine synthase activity / cobalamin binding / methylation / zinc ion binding
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
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 11, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2May 1, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methionine synthase
C: Methionine synthase
B: Methionine synthase


Theoretical massNumber of molelcules
Total (without water)175,8163
Polymers175,8163
Non-polymers00
Water8,737485
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.177, 96.177, 356.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 58605.441 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA0618 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKM5, methionine synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M Sodium Acetate, pH 4.6, 2 M Sodium Formate

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2022
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing, with two horizontally deflecting mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.8314
pseudo-merohedral22-h,-k,l20.1686
ReflectionResolution: 2.4→40.55 Å / Num. obs: 76051 / % possible obs: 100 % / Redundancy: 9.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.061 / Rrim(I) all: 0.187 / Χ2: 0.92 / Net I/σ(I): 8.1 / Num. measured all: 711608
Reflection shellResolution: 2.4→2.45 Å / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.903 / Num. measured all: 42258 / Num. unique obs: 4396 / CC1/2: 0.667 / Rpim(I) all: 0.306 / Rrim(I) all: 0.954 / Χ2: 0.92 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BUL

3bul


Resolution: 2.4→39.85 Å / Cor.coef. Fo:Fc: 0.863 / Cor.coef. Fo:Fc free: 0.829 / SU B: 8.23 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.065
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.301 3829 5.042 %RANDOM
Rwork0.265 ---
obs-75947 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.88 Å2
Baniso -1Baniso -2Baniso -3
1--4.612 Å20 Å20 Å2
2---4.612 Å20 Å2
3---9.224 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11959 0 0 485 12444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01212252
X-RAY DIFFRACTIONr_bond_other_d0.0040.01611784
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.65216565
X-RAY DIFFRACTIONr_angle_other_deg0.7491.56827082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.58951506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.4555109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.493102075
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.21761
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214493
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022887
X-RAY DIFFRACTIONr_nbd_refined0.1230.21852
X-RAY DIFFRACTIONr_nbd_other0.0970.2143
X-RAY DIFFRACTIONr_nbtor_refined0.1360.25483
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0680.2387
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_it2.6224.596045
X-RAY DIFFRACTIONr_mcbond_other2.6214.596045
X-RAY DIFFRACTIONr_mcangle_it4.1768.317541
X-RAY DIFFRACTIONr_mcangle_other4.1758.3117542
X-RAY DIFFRACTIONr_scbond_it2.4234.7916207
X-RAY DIFFRACTIONr_scbond_other2.4234.7916206
X-RAY DIFFRACTIONr_scangle_it3.9588.7449023
X-RAY DIFFRACTIONr_scangle_other3.9588.7459024
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å
RfactorNum. reflection% reflection
Rfree0.322 273 -
Rwork0.249 5241 -
obs--99.76 %

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