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- PDB-2yci: methyltransferase native -

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Basic information

Entry
Database: PDB / ID: 2yci
Titlemethyltransferase native
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-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase
Similarity search - Component
Biological speciesCARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 / Other / 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 "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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,4544
Polymers30,1661
Non-polymers2883
Water4,035224
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)60,9088
Polymers60,3322
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4090 Å2
ΔGint-91.2 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.009, 64.009, 176.178
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: 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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.99 Å3/Da / Density % sol: 58.88 % / 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: 1.78→100 Å / Num. obs: 35890 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.03
Reflection shellResolution: 1.78→1.83 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.79 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→19.2 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.902 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23357 1795 5 %RANDOM
Rwork0.19066 ---
obs0.19281 34093 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.099 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å20 Å2
2--1.49 Å20 Å2
3----2.98 Å2
Refinement stepCycle: LAST / Resolution: 1.78→19.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 15 224 2346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222170
X-RAY DIFFRACTIONr_bond_other_d0.0010.021450
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.9772951
X-RAY DIFFRACTIONr_angle_other_deg0.92933565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0955274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.42524.89696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85715384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4781514
X-RAY DIFFRACTIONr_chiral_restr0.1410.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0260.0212393
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02390
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2221.51364
X-RAY DIFFRACTIONr_mcbond_other1.2081.5540
X-RAY DIFFRACTIONr_mcangle_it4.42722211
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.4743806
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.1824.5738
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 129 -
Rwork0.321 2456 -
obs--100 %

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