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- PDB-3bol: Cobalamin-dependent methionine synthase (1-566) from Thermotoga m... -

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Basic information

Entry
Database: PDB / ID: 3bol
TitleCobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+
Components5-methyltetrahydrofolate S-homocysteine methyltransferase
KeywordsTRANSFERASE / MetH / TIM BARREL / ZINC / ZINC INVERSION / Methyltransferase
Function / homology
Function and homology information


methionine synthase / methionine synthase activity / homocysteine metabolic process / methionine biosynthetic process / cobalamin binding / tetrahydrofolate metabolic process / methylation / metal ion binding / cytosol
Similarity search - Function
5-methyltetrahydrofolate-homocysteine S-methyltransferase, bacterial / Homocysteine-binding-like domain / 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 ...5-methyltetrahydrofolate-homocysteine S-methyltransferase, bacterial / Homocysteine-binding-like domain / 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 / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-AMINO-4-MERCAPTO-BUTYRIC ACID / : / YTTRIUM (III) ION / Methionine synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsKoutmos, M. / Smith, J.L. / Ludwig, M.L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Metal active site elasticity linked to activation of homocysteine in methionine synthases.
Authors: Koutmos, M. / Pejchal, R. / Bomer, T.M. / Matthews, R.G. / Smith, J.L. / Ludwig, M.L.
History
DepositionDec 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-methyltetrahydrofolate S-homocysteine methyltransferase
B: 5-methyltetrahydrofolate S-homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,7659
Polymers127,2662
Non-polymers4997
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.626, 85.841, 125.587
Angle α, β, γ (deg.)90.000, 100.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 5-methyltetrahydrofolate S-homocysteine methyltransferase


Mass: 63633.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21 DE3 / References: UniProt: Q9WYA5, methionine synthase

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Non-polymers , 5 types, 361 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Y
#5: Chemical ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 25% 1,2-propanediol, 10% glycerol, 5% PEG 3000, 100 mM potasium citrate pH 4.8, 1.5% 1,2,3-heptanetriol, 10 mM YCl3. Soaking with 20% 1,2-propanediol, 10% glycerol, 5% PEG 3000, 100 mM TRIS ...Details: 25% 1,2-propanediol, 10% glycerol, 5% PEG 3000, 100 mM potasium citrate pH 4.8, 1.5% 1,2,3-heptanetriol, 10 mM YCl3. Soaking with 20% 1,2-propanediol, 10% glycerol, 5% PEG 3000, 100 mM TRIS pH 7, and 1.5% 1,2,3-heptanetriol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / 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: 1.85→47.62 Å / Num. all: 106175 / Num. obs: 106165 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 31.916 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.062 / Net I/σ(I): 21.65
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 5.6 / Num. measured obs: 126216 / Num. unique all: 16806 / Num. unique obs: 16806 / Rsym value: 0.417 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Translation4.5 Å50 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
EPMRphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
Blu-Icedata collection
XDSdata reduction
CNS1.2 / REFMAC 5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→47.62 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.901 / SU ML: 0.089 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.136 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 5351 5 %RANDOM
Rwork0.193 ---
obs0.195 106164 99.99 %-
all-106175 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.964 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20.34 Å2
2--0.54 Å20 Å2
3----1.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.128 Å0.136 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.85→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8687 0 14 354 9055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228857
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9911968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08451101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82924.175388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53151604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7071558
X-RAY DIFFRACTIONr_chiral_restr0.110.21371
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026595
X-RAY DIFFRACTIONr_nbd_refined0.2190.24375
X-RAY DIFFRACTIONr_nbtor_refined0.3130.26180
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2487
X-RAY DIFFRACTIONr_metal_ion_refined0.110.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.213
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1330.21
X-RAY DIFFRACTIONr_mcbond_it0.9841.55498
X-RAY DIFFRACTIONr_mcangle_it1.8128894
X-RAY DIFFRACTIONr_scbond_it2.82333392
X-RAY DIFFRACTIONr_scangle_it4.7334.53074
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 414 -
Rwork0.228 7405 -
all-7819 -
obs--100 %

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