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

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Basic information

Entry
Database: PDB / ID: 3bof
TitleCobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+ and Homocysteine
Components5-methyltetrahydrofolate S-homocysteine methyltransferase
KeywordsTRANSFERASE / MetH / TIM BARREL / HOMOCYSTEINE / 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 / B12 binding 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: 1.7 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)127,8359
Polymers127,2662
Non-polymers5687
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.067, 86.308, 125.879
Angle α, β, γ (deg.)90.000, 100.030, 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, 418 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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 / Yttrium


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 / Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 50.46 %
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, 1.5% 1,2,3-heptanetriol, and 10mM Hcy , 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: 1.7→46.68 Å / Num. all: 136668 / Num. obs: 136540 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 28.911 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.048 / Net I/σ(I): 22.5
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 5.36 / Num. unique all: 21423 / Rsym value: 0.399 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
EPMRphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
Blu-Icedata collection
XDSdata reduction
CNS1.2 / REFMAC 5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→46.68 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.082 / SU ML: 0.07 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.222 6933 5.1 %RANDOM
Rwork0.195 ---
obs0.196 136540 99.91 %-
all-136668 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.688 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.102 Å0.106 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.7→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8763 0 21 411 9195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228942
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.9912084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67951113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93624.184392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.951151613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8811558
X-RAY DIFFRACTIONr_chiral_restr0.10.21382
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026662
X-RAY DIFFRACTIONr_nbd_refined0.2150.24414
X-RAY DIFFRACTIONr_nbtor_refined0.3110.26274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2522
X-RAY DIFFRACTIONr_metal_ion_refined0.0830.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.211
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0430.21
X-RAY DIFFRACTIONr_mcbond_it0.8641.55546
X-RAY DIFFRACTIONr_mcangle_it1.60628971
X-RAY DIFFRACTIONr_scbond_it2.48333419
X-RAY DIFFRACTIONr_scangle_it4.1764.53113
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 543 -
Rwork0.236 9517 -
all-10060 -
obs--99.93 %

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