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- PDB-1k98: AdoMet complex of MetH C-terminal fragment -

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Basic information

Entry
Database: PDB / ID: 1k98
TitleAdoMet complex of MetH C-terminal fragment
ComponentsMethionine synthase
KeywordsTRANSFERASE / AdoMet binding / MOTION OF 4-HELIX BUNDLE / DOMAIN INTERACTIONS
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 / cytoplasm / cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 3.75 Å
AuthorsBandarian, V. / Pattridge, K.A. / Lennon, B.W. / Huddler, D.P. / Matthews, R.G. / Ludwig, M.L.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Domain alternation switches B(12)-dependent methionine synthase to the activation conformation.
Authors: Bandarian, V. / Pattridge, K.A. / Lennon, B.W. / Huddler, D.P. / Matthews, R.G. / Ludwig, M.L.
History
DepositionOct 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Non-polymer description
Revision 1.4Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Oct 27, 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 1.6Aug 16, 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)66,2863
Polymers64,8591
Non-polymers1,4262
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.503, 108.503, 146.474
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Methionine synthase


Mass: 64859.137 Da / Num. of mol.: 1 / Fragment: c-terminal activation complex, residues 651-1227 / Mutation: H759G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P13009, methionine synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / 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: 3.32 Å3/Da / Density % sol: 62.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: cacodylate, ammonium sulfate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
20.1 Mcacodylate1reservoirpH6.5
30.2 Mammonium sulfate1reservoir
430 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 9, 2000 / Details: Yale mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.75→50 Å / Num. all: 8076 / Num. obs: 8076 / % possible obs: 86.8 % / Observed criterion σ(I): 0 / Rsym value: 0.063
Reflection shellResolution: 3.75→3.88 Å / Rsym value: 0.451 / % possible all: 66.9
Reflection
*PLUS
Lowest resolution: 35 Å / Num. obs: 8057 / % possible obs: 85.1 % / Num. measured all: 34361 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 62.8 % / Rmerge(I) obs: 0.444

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1k7y

1k7y


Resolution: 3.75→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.363 422 -random
Rwork0.308 ---
all0.311 7901 --
obs0.311 7901 5.3 %-
Refinement stepCycle: LAST / Resolution: 3.75→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4566 0 96 0 4662
LS refinement shellResolution: 3.75→3.88 Å /
RfactorNum. reflection
Rfree0.48 23
Rwork0.478 -
obs-474
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.308
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.97
LS refinement shell
*PLUS
Rfactor Rfree: 0.48 / Rfactor Rwork: 0.478

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