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- PDB-1y8c: Crystal structure of a S-adenosylmethionine-dependent methyltrans... -

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Basic information

Entry
Database: PDB / ID: 1y8c
TitleCrystal structure of a S-adenosylmethionine-dependent methyltransferase from Clostridium acetobutylicum ATCC 824
ComponentsS-adenosylmethionine-dependent methyltransferase
KeywordsTRANSFERASE / Structural Genomics / Protein Structure Initiative / PSI / NYSGXRC / New York SGX Research Center for Structural Genomics / T1987 / CAC2371 / methyltransferase
Function / homology
Function and homology information


methyltransferase activity / methylation
Similarity search - Function
S-adenosyl-L-methionine-dependent methyltransferases / : / Methyltransferase domain 25 / Methyltransferase domain / N-terminal domain of TfIIb / Single Sheet / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich ...S-adenosyl-L-methionine-dependent methyltransferases / : / Methyltransferase domain 25 / Methyltransferase domain / N-terminal domain of TfIIb / Single Sheet / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-adenosylmethionine-dependent methyltransferase
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsRajashankar, K.R. / Kniewel, R. / Lee, K. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a S-adenosylmethionine-dependent methyltransferase from Clostridium acetobutylicum ATCC 824
Authors: Rajashankar, K.R. / Kniewel, R. / Lee, K. / Lima, C.D.
History
DepositionDec 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _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 1.4Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_starting_model
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-adenosylmethionine-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4282
Polymers29,3321
Non-polymers961
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.918, 67.918, 134.499
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

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Components

#1: Protein S-adenosylmethionine-dependent methyltransferase / AM dependent methyltransferase


Mass: 29331.541 Da / Num. of mol.: 1 / Fragment: SAM dependent methyltransferase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Strain: ATCC 824 / Gene: CAC2371, 1118554 / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834, DE3 / References: UniProt: Q97GJ5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.6M Ammonium Sulfate, 0.1M Potassium Phosphate Monobasic, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTAM Q315 / Detector: CCD / Date: Nov 6, 2004
Details: Vertical focussing mirror down stream of monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 23695 / Num. obs: 23695 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 37.3 Å2 / Rsym value: 0.057 / Net I/σ(I): 22.7
Reflection shellResolution: 2.5→2.59 Å / Num. unique all: 2307 / Rsym value: 0.362 / % possible all: 96.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 2.5→44.27 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 359501.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: No clear density was observed for Tyr4 side chain. Hence it was modelled as Ser.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1084 4.9 %RANDOM
Rwork0.221 ---
all0.2211 12392 --
obs0.2211 12392 91.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.4609 Å2 / ksol: 0.375655 e/Å3
Displacement parametersBiso mean: 64.1 Å2
Baniso -1Baniso -2Baniso -3
1-16.65 Å213.22 Å20 Å2
2--16.65 Å20 Å2
3----33.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.5→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 5 50 2109
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.462.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 150 5 %
Rwork0.398 2847 -
obs--75.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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