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- PDB-2ycj: methyltransferase bound with methyltetrahydrofolate -

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Basic information

Entry
Database: PDB / ID: 2ycj
Titlemethyltransferase bound with methyltetrahydrofolate
Components5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


pteridine-containing compound metabolic process / methyltransferase activity / methylation / metal ion binding
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
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase
Similarity search - Component
Biological speciesCARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,38210
Polymers30,1661
Non-polymers1,2169
Water2,936163
1
A: 5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)62,76420
Polymers60,3322
Non-polymers2,43218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7970 Å2
ΔGint-127.3 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.702, 64.702, 177.302
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 / METHYLTRANSFERASE


Mass: 30165.889 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


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID


Mass: 459.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N7O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.08 Å3/Da / Density % sol: 60.01 % / 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: 1.96→35 Å / Num. obs: 27851 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 34.75 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 27.46
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.34 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→32.351 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 1392 5 %
Rwork0.2003 --
obs0.2022 27843 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.476 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.8695 Å20 Å20 Å2
2--5.8695 Å20 Å2
3----3.2167 Å2
Refinement stepCycle: LAST / Resolution: 1.96→32.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 76 163 2346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082248
X-RAY DIFFRACTIONf_angle_d1.3293058
X-RAY DIFFRACTIONf_dihedral_angle_d14.853844
X-RAY DIFFRACTIONf_chiral_restr0.103345
X-RAY DIFFRACTIONf_plane_restr0.007393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.03010.32021360.28462575X-RAY DIFFRACTION100
2.0301-2.11130.36851340.28092559X-RAY DIFFRACTION99
2.1113-2.20740.31231370.25172597X-RAY DIFFRACTION100
2.2074-2.32380.26651370.23092616X-RAY DIFFRACTION100
2.3238-2.46930.30621370.22212606X-RAY DIFFRACTION99
2.4693-2.65990.28331380.22462624X-RAY DIFFRACTION100
2.6599-2.92740.25771390.21792637X-RAY DIFFRACTION100
2.9274-3.35060.25851400.20722659X-RAY DIFFRACTION100
3.3506-4.21990.18681420.17062710X-RAY DIFFRACTION100
4.2199-32.35540.2021520.17222868X-RAY DIFFRACTION99

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