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- PDB-1u1j: A. thaliana cobalamine independent methionine synthase -

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Basic information

Entry
Database: PDB / ID: 1u1j
TitleA. thaliana cobalamine independent methionine synthase
Components5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
KeywordsTRANSFERASE / METHIONINE / SYNTHASE / HOMOCYSTEINE / METHYLTETRAHYDROFOLATE
Function / homology
Function and homology information


: / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / methionine synthase activity / 'de novo' L-methionine biosynthetic process / plasmodesma / plant-type vacuole / apoplast / DNA methylation-dependent heterochromatin formation / methionine biosynthetic process ...: / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / methionine synthase activity / 'de novo' L-methionine biosynthetic process / plasmodesma / plant-type vacuole / apoplast / DNA methylation-dependent heterochromatin formation / methionine biosynthetic process / chloroplast stroma / response to zinc ion / chloroplast / peroxisome / methylation / copper ion binding / mRNA binding / zinc ion binding / plasma membrane / cytosol
Similarity search - Function
Cobalamin-independent methionine synthase / Cobalamin-independent methionine synthase MetE, N-terminal / Cobalamin-independent synthase, N-terminal domain / Cobalamin-independent methionine synthase MetE, C-terminal/archaeal / Cobalamin-independent synthase, Catalytic domain / TIM Barrel - #210 / UROD/MetE-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / METHIONINE / 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsFerrer, J.-L. / Ravanel, S. / Robert, M. / Dumas, R.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structures of cobalamin-independent methionine synthase complexed with zinc, homocysteine, and methyltetrahydrofolate
Authors: Ferrer, J.-L. / Ravanel, S. / Robert, M. / Dumas, R.
History
DepositionJul 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4919
Polymers85,3681
Non-polymers1,1248
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.465, 123.465, 132.721
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase / Vitamin-B12-independent methionine synthase isozyme / Cobalamin-independent methionine synthase isozyme


Mass: 85367.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CIMS / Plasmid: PET-MS1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O50008, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase

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Non-polymers , 5 types, 291 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#5: Chemical ChemComp-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / Levomefolic acid


Mass: 459.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N7O6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 3.37 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% (W/V) POLY-ETHYLENE GLYCOL (PEG) 8000, 0.2 M AMMONIUM SULFATE, 1 MM DTT AND 0.1 M SODIUM CACODYLATE, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 / Wavelength: 0.933 Å
DetectorType: ADSC / Detector: CCD / Date: Jun 15, 2004
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 45073 / Num. obs: 44622 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.97 % / Biso Wilson estimate: 42.2 Å2 / Rsym value: 0.089 / Net I/σ(I): 12.25
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 5.95 % / Mean I/σ(I) obs: 2.37 / Num. unique all: 7080 / Rsym value: 0.563 / % possible all: 97.8

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Processing

Software
NameClassification
XDSdata scaling
XSCALEdata scaling
CNSrefinement
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1U1H
Resolution: 2.4→41.63 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3207526.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.275 4120 9.2 %RANDOM
Rwork0.215 ---
all0.218 45055 --
obs0.215 44551 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 83.7242 Å2 / ksol: 0.341786 e/Å3
Displacement parametersBiso mean: 63.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.92 Å26.29 Å20 Å2
2--5.92 Å20 Å2
3----11.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.4→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5783 0 64 283 6130
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_scangle_it2.672.5
LS refinement shellResolution: 2.4→2.51 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.364 506 9.1 %
Rwork0.351 5039 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4MTF_PAR.TXTMTF_TOP.TXT

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