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- PDB-3dli: Crystal structure of a SAM dependent methyltransferase from Archa... -

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Basic information

Entry
Database: PDB / ID: 3dli
TitleCrystal structure of a SAM dependent methyltransferase from Archaeoglobus fulgidus
Componentsmethyltransferase
KeywordsTRANSFERASE / 11116b / PSI-II / NYSGXRC / methyltransferase / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homologyMethyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.46 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 Archaeoglobus fulgidus
Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S.
History
DepositionJun 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 10, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 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: methyltransferase
B: methyltransferase
C: methyltransferase


Theoretical massNumber of molelcules
Total (without water)84,4693
Polymers84,4693
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-62 kcal/mol
Surface area28810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.154, 81.880, 122.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein methyltransferase


Mass: 28156.371 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF_0046 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIPL / References: UniProt: O30190
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium sulfate, 0.1M Bis-tris, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2008 / Details: Mirrors
RadiationMonochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.46→50 Å / Num. all: 28155 / Num. obs: 28155 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9
Reflection shellResolution: 2.46→2.55 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / Num. unique all: 2757 / % possible all: 100

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Processing

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

Resolution: 2.46→41.12 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 71812.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 789 2.9 %RANDOM
Rwork0.23 ---
all0.25 28155 --
obs0.23 27297 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.3972 Å2 / ksol: 0.375567 e/Å3
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.97 Å20 Å20 Å2
2--5.79 Å20 Å2
3----0.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.46→41.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 0 0 157 5647
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 2.46→2.61 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 119 2.8 %
Rwork0.283 4092 -
obs-28155 91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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