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- PDB-3iva: Structure of the B12-dependent Methionine Synthase (MetH) C-temin... -

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Basic information

Entry
Database: PDB / ID: 3iva
TitleStructure of the B12-dependent Methionine Synthase (MetH) C-teminal half with AdoHcy bound
ComponentsMethionine synthase
KeywordsTRANSFERASE / METH / reactivation conformation / H759 / cobalamin / intermodular interactions / amino-acid biosynthesis / cobalt / metal-binding / methionine biosynthesis / methyltransferase / S-adenosyl-L-methionine / S-adenosyl-homocysteine
Function / homology
Function and homology information


methionine synthase / methionine synthase activity / homocysteine metabolic process / cobalamin binding / tetrahydrofolate metabolic process / methionine biosynthetic 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 / NITRATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Methionine synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPattridge, K.A. / Koutmos, M. / Smith, J.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Insights into the reactivation of cobalamin-dependent methionine synthase.
Authors: Koutmos, M. / Datta, S. / Pattridge, K.A. / Smith, J.L. / Matthews, R.G.
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 24, 2012Group: Non-polymer description
Revision 1.3Oct 13, 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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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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)67,1387
Polymers65,1761
Non-polymers1,9636
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.006, 107.006, 141.185
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 / 5-methyltetrahydrofolate--homocysteine methyltransferase / Methionine synthase / vitamin-B12-dependent / MS


Mass: 65175.504 Da / Num. of mol.: 1
Fragment: C-terminal activation complex (UNP residues 649-1227)
Mutation: I690C, G743C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b4019, JW3979, metH / Plasmid: PVB8 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P13009, methionine synthase
#2: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 60.4 %
Crystal growTemperature: 302 K / Method: vapor diffusion / pH: 7
Details: 0.2 M potassium nitrate, 18 % (w/v) PEG3350, pH 7.0, VAPOR DIFFUSION, temperature 302K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 2, 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: 2.7→50 Å / Num. all: 23160 / Num. obs: 23160 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.4 % / Rmerge(I) obs: 0.043 / Rsym value: 0.085 / Net I/σ(I): 27.3
Reflection shellResolution: 2.7→2.86 Å / Redundancy: 22.4 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 5.82 / Rsym value: 0.622 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-IceEpicsdata collection
EPMRphasing
CNS1.2refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Individual domains of PDB entry 3BUL

3bul


Resolution: 2.7→45.32 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 3333675.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1130 4.9 %RANDOM
Rwork0.246 ---
obs0.246 23159 99.9 %-
all-23159 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.9901 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 76.7 Å2
Baniso -1Baniso -2Baniso -3
1--6.58 Å20 Å20 Å2
2---6.58 Å20 Å2
3---13.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.7→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4563 0 133 26 4722
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d4.32
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.652
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.982.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 169 4.5 %
Rwork0.311 3588 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4param12cns.kaptopcns.cob3
X-RAY DIFFRACTION5ligands.paramligands.top

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