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- PDB-3dh0: Crystal structure of a SAM dependent methyltransferase from Aquif... -

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Basic information

Entry
Database: PDB / ID: 3dh0
TitleCrystal structure of a SAM dependent methyltransferase from Aquifex aeolicus
ComponentsSAM dependent methyltransferase
KeywordsTRANSFERASE / Cystal structure / PSI-2 / NYSGXRC / 11116c / SAM dependent / methyltransferase / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


methyltransferase activity
Similarity search - Function
Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Methyltransferase domain-containing protein
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.72 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a SAM dependent methyltransferase from Aquifex aeolicus
Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S.
History
DepositionJun 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAM dependent methyltransferase
B: SAM dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1014
Polymers50,3042
Non-polymers7972
Water84747
1
A: SAM dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5502
Polymers25,1521
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SAM dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5502
Polymers25,1521
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.436, 42.902, 84.253
Angle α, β, γ (deg.)90.00, 106.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SAM dependent methyltransferase


Mass: 25152.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1457 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: O67440
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 2M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 8, 2008 / Details: mirrors
RadiationMonochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.72→50 Å / Num. all: 12492 / Num. obs: 12492 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 60.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.7
Reflection shellResolution: 2.72→2.82 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2 / Num. unique all: 1209 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: None

Resolution: 2.72→40.34 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 106026.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 366 3 %RANDOM
Rwork0.231 ---
obs0.231 12244 97.9 %-
all-12492 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.9192 Å2 / ksol: 0.357554 e/Å3
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1--13.82 Å20 Å2-0.19 Å2
2--18.92 Å20 Å2
3----5.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.72→40.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3053 0 54 47 3154
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d1
LS refinement shellResolution: 2.72→2.89 Å / Rfactor Rfree error: 0.066 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.458 48 2.5 %
Rwork0.313 1887 -
obs-12492 94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramsam.top
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4sam.param

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