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- PDB-3bul: E. coli I690C/G743C MetH C-terminal fragment (649-1227) -

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Basic information

Entry
Database: PDB / ID: 3bul
TitleE. coli I690C/G743C MetH C-terminal fragment (649-1227)
ComponentsMethionine synthase
KeywordsTRANSFERASE / MetH / REACTIVATION CONFORMATION / H759 / COBALAMIN / INTERMODULAR INTERACTIONS / Amino-acid biosynthesis / Cobalt / Metal-binding / Methionine biosynthesis / Methyltransferase / S-adenosyl-L-methionine
Function / homology
Function and homology information


methionine synthase / methionine synthase activity / homocysteine metabolic process / methionine biosynthetic process / cobalamin binding / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / methylation / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Cobalamin-dependent Methionine Synthase; domain 2 / Cobalamin-dependent Methionine Synthase, domain 2 / Cobalamin-dependent Methionine Synthase; domain 1 / Vitamin B12-dependent methionine synthase, activation domain / Methionine synthase domain / 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 ...Cobalamin-dependent Methionine Synthase; domain 2 / Cobalamin-dependent Methionine Synthase, domain 2 / Cobalamin-dependent Methionine Synthase; domain 1 / Vitamin B12-dependent methionine synthase, activation domain / Methionine synthase domain / 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-binding domain / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / 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 / Roll / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COBALAMIN / Methionine synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsKoutmos, M. / Pattridge, K.A. / Ludwig, M.L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: A disulfide-stabilized conformer of methionine synthase reveals an unexpected role for the histidine ligand of the cobalamin cofactor.
Authors: Datta, S. / Koutmos, M. / Pattridge, K.A. / Ludwig, M.L. / Matthews, R.G.
History
DepositionJan 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 24, 2012Group: Non-polymer description
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5062
Polymers65,1761
Non-polymers1,3301
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.529, 106.529, 137.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Methionine synthase / / 5-methyltetrahydrofolate-homocysteine methyltransferase / Methionine synthase / vitamin-B12- dependent / MS


Mass: 65175.504 Da / Num. of mol.: 1 / Fragment: C-terminal activation complex (residues 649-1227) / Mutation: I690C, G743C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: metH / Plasmid: pVB8 / Production host: Escherichia coli (E. coli) / Strain (production host): Hms174(DE3) / References: UniProt: P13009, methionine synthase
#2: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.99 Å3/Da / Density % sol: 58.92 %
Crystal growTemperature: 310 K / Method: evaporation / pH: 7.2
Details: 0.2 M potassium nitrate, and 20 % (w/v) PEG3350, pH 7.2, EVAPORATION, temperature 310K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 1, 2007
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.29→42.07 Å / Num. obs: 35908 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.306 % / Biso Wilson estimate: 42.722 Å2 / Rmerge(I) obs: 0.146 / Rsym value: 0.151 / Net I/σ(I): 16
Reflection shellResolution: 2.29→2.43 Å / Redundancy: 15.01 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 3.46 / Num. measured obs: 82804 / Num. unique all: 5516 / Num. unique obs: 5516 / Rsym value: 0.838 / % possible all: 95.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Translation4 Å50 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
EPMRphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K7Y

1k7y


Resolution: 2.3→42.07 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.715 / SU ML: 0.163 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.259 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1773 5 %RANDOM
Rwork0.198 ---
all0.228 35738 --
obs0.2 35737 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.387 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.215 Å0.259 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2.3→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4572 0 91 63 4726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0224773
X-RAY DIFFRACTIONr_angle_refined_deg2.3181.9786506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7175576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.63824.323229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.62615794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1261533
X-RAY DIFFRACTIONr_chiral_restr0.2340.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023667
X-RAY DIFFRACTIONr_nbd_refined0.2510.22297
X-RAY DIFFRACTIONr_nbtor_refined0.3230.23340
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2189
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.22
X-RAY DIFFRACTIONr_mcbond_it1.361.52950
X-RAY DIFFRACTIONr_mcangle_it2.27124635
X-RAY DIFFRACTIONr_scbond_it3.58532097
X-RAY DIFFRACTIONr_scangle_it5.5494.51871
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 124 -
Rwork0.262 2484 -
all-2608 -
obs--99.96 %

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