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- PDB-2yck: methyltransferase bound with tetrahydrofolate -

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Basic information

Entry
Database: PDB / ID: 2yck
Titlemethyltransferase bound with tetrahydrofolate
Components5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE
KeywordsTRANSFERASE / TIM-BARREL / VITAMIN B12
Function / homology
Function and homology information


pteridine-containing compound metabolic process / methyltransferase activity / methylation
Similarity search - Function
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
(6S)-5,6,7,8-TETRAHYDROFOLATE / 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase
Similarity search - Component
Biological speciesCARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGoetzl, S. / Jeoung, J.-H. / Hennig, S.E. / Dobbek, H.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural Basis for Electron and Methyl-Group Transfer in a Methyltransferase System Operating in the Reductive Acetyl-Coa Pathway
Authors: Goetzl, S. / Jeoung, J.-H. / Hennig, S.E. / Dobbek, H.
History
DepositionMar 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references / Non-polymer description / Version format compliance
Revision 1.2May 16, 2012Group: Other
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: 5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,43310
Polymers30,2231
Non-polymers1,2109
Water2,288127
1
X: 5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE
hetero molecules

X: 5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,86620
Polymers60,4462
Non-polymers2,42018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7260 Å2
ΔGint-166.4 kcal/mol
Surface area22270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.955, 63.955, 175.095
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein 5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE


Mass: 30222.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
Strain: Z-2901 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3ACR9
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.48 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9814
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 2.15→35 Å / Num. obs: 20410 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.45
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.59 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→27.187 Å / SU ML: 0.31 / σ(F): 1.99 / Phase error: 21.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2303 1021 5 %
Rwork0.1776 --
obs0.1803 20407 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.632 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.0458 Å20 Å20 Å2
2--6.0458 Å20 Å2
3----0.1295 Å2
Refinement stepCycle: LAST / Resolution: 2.15→27.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 73 127 2311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072230
X-RAY DIFFRACTIONf_angle_d1.0553033
X-RAY DIFFRACTIONf_dihedral_angle_d16.971856
X-RAY DIFFRACTIONf_chiral_restr0.068339
X-RAY DIFFRACTIONf_plane_restr0.006391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.26330.28051430.24022715X-RAY DIFFRACTION99
2.2633-2.4050.3071430.22742715X-RAY DIFFRACTION100
2.405-2.59060.28961440.23072734X-RAY DIFFRACTION99
2.5906-2.8510.27841440.22042740X-RAY DIFFRACTION99
2.851-3.2630.25491440.19472740X-RAY DIFFRACTION99
3.263-4.10880.20261470.15722781X-RAY DIFFRACTION98
4.1088-27.18960.19731560.14682961X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 2.5303 Å / Origin y: 6.1593 Å / Origin z: 18.7721 Å
111213212223313233
T0.2258 Å20.0278 Å2-0.0091 Å2-0.3466 Å2-0.0031 Å2--0.2504 Å2
L1.4126 °2-0.2021 °2-0.7138 °2-1.0195 °2-0.1248 °2--1.219 °2
S-0.0049 Å °-0.3284 Å °-0.0571 Å °0.0549 Å °-0.1028 Å °0.012 Å °0.1787 Å °0.1202 Å °0.0943 Å °
Refinement TLS groupSelection details: (CHAIN X AND RESID -8:263)

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