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- PDB-1q8a: Cobalamin-dependent methionine synthase (1-566) from Thermotoga m... -

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Basic information

Entry
Database: PDB / ID: 1q8a
TitleCobalamin-dependent methionine synthase (1-566) from Thermotoga maritima (Cd2+:L-Hcy complex, Se-Met)
Components5-methyltetrahydrofolate S-homocysteine methyltransferase
KeywordsTRANSFERASE / homocysteine / methionine / folate / cobalamin / vitamin b12
Function / homology
Function and homology information


methionine synthase / methionine synthase activity / homocysteine metabolic process / cobalamin binding / tetrahydrofolate metabolic process / methionine biosynthetic 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 / Dihydropteroate synthase-like / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / 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 / Methionine synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsEvans, J.C. / Huddler, D.P. / Hilgers, M.T. / Romanchuk, G. / Matthews, R.G. / Ludwig, M.L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Structures of the N-terminal modules imply large domain motions during catalysis by methionine synthase.
Authors: Evans, J.C. / Huddler, D.P. / Hilgers, M.T. / Romanchuk, G. / Matthews, R.G. / Ludwig, M.L.
History
DepositionAug 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)128,6996
Polymers128,2042
Non-polymers4954
Water4,197233
1
A: 5-methyltetrahydrofolate S-homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3503
Polymers64,1021
Non-polymers2482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5-methyltetrahydrofolate S-homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3503
Polymers64,1021
Non-polymers2482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.120, 86.190, 126.080
Angle α, β, γ (deg.)90.00, 99.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 5-methyltetrahydrofolate S-homocysteine methyltransferase


Mass: 64102.102 Da / Num. of mol.: 2 / Fragment: MetH_Tm (residues 1-566)
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
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


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


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: propylene glycol, glycerol, PEG 8000, citrate, 1,2,3-heptanetriol, cadmium, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mM1dropCdCl2
21.25 %(w/v)1,2,3-heptanetriol1drop
325 %1,2-propanediol1reservoir
410 %glycerol1reservoir
55 %PEG30001reservoir
6100 mMsodium citrate1reservoirpH5.30

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 136760 / Num. obs: 125901 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.78 Å / % possible all: 83.7
Reflection
*PLUS
Highest resolution: 1.65 Å / Num. obs: 147923 / % possible obs: 99.4 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.96

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.242 12710 RANDOM THROUGHOUT
Rwork0.214 --
all0.225 136760 -
obs0.225 125901 -
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8756 0 18 233 9007
Refinement
*PLUS
Highest resolution: 1.65 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.0131
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.687

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