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- PDB-1t7l: Crystal Structure of Cobalamin-Independent Methionine Synthase fr... -

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Basic information

Entry
Database: PDB / ID: 1t7l
TitleCrystal Structure of Cobalamin-Independent Methionine Synthase from T. maritima
Components5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
KeywordsTRANSFERASE / TIM BARREL / HOMOCYSTEINE / METHYLTETRAHYDROFOLATE / ZINC
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 / methylation / zinc ion binding / extracellular region / 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
MESO-ERYTHRITOL / 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPejchal, R. / Ludwig, M.L.
CitationJournal: Plos Biol. / Year: 2005
Title: Cobalamin-independent methionine synthase (MetE): a face-to-face double barrel that evolved by gene duplication
Authors: Pejchal, R. / Ludwig, M.L.
History
DepositionMay 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)179,2576
Polymers178,8212
Non-polymers4364
Water11,133618
1
A: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6283
Polymers89,4101
Non-polymers2182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6283
Polymers89,4101
Non-polymers2182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.565, 158.763, 64.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 89410.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: METE, TM1286 / Plasmid: PET-151-D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3)
References: UniProt: Q9X112, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MRY / MESO-ERYTHRITOL


Mass: 122.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 295 K / Method: vapor batch, under oil / pH: 4.6
Details: PEG 4000, sodium acetate, ammonium sulfate, pH 4.6, VAPOR BATCH, UNDER OIL, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→19.91 Å / Num. all: 112572 / Num. obs: 112572 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.081 / Net I/σ(I): 13.77
Reflection shellResolution: 2→2.1 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 4.35 / Num. unique all: 14848 / Rsym value: 0.381 / % possible all: 97.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
XDSdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.91 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3599544.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: molecular replacement model derived from experimental model based on Se SAD phases
RfactorNum. reflection% reflectionSelection details
Rfree0.24 11263 10 %RANDOM
Rwork0.206 ---
all0.226 112572 --
obs0.206 112572 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.9798 Å2 / ksol: 0.363465 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--2.96 Å20 Å2
3----3.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11611 0 26 618 12255
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 1833 10.1 %
Rwork0.242 16382 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2MERY.PARAMMERY.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5PARAM.SO4TOPH.SO4

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