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- PDB-2h1r: Crystal structure of a dimethyladenosine transferase from Plasmod... -

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Basic information

Entry
Database: PDB / ID: 2h1r
TitleCrystal structure of a dimethyladenosine transferase from Plasmodium falciparum
ComponentsDimethyladenosine transferase, putative
KeywordsTRANSFERASE / SGC Toronto dimethyladenosine transferase / Structural Genomics / Structural Genomics Consortium
Function / homology
Function and homology information


Mitochondrial transcription initiation / rRNA modification / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA methyltransferase activity / rRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / RNA binding
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #480 / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Helicase, Ruva Protein; domain 3 - #480 / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
rRNA adenine N(6)-methyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsDong, A. / Lew, J. / Ren, H. / Sundararajan, E. / Zhao, Y. / Wasney, G. / Vedadi, M. / Kozieradski, I. / Edwards, A.M. / Arrowsmith, C.H. ...Dong, A. / Lew, J. / Ren, H. / Sundararajan, E. / Zhao, Y. / Wasney, G. / Vedadi, M. / Kozieradski, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Qiu, W. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionMay 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dimethyladenosine transferase, putative
B: Dimethyladenosine transferase, putative


Theoretical massNumber of molelcules
Total (without water)69,2792
Polymers69,2792
Non-polymers00
Water8,971498
1
A: Dimethyladenosine transferase, putative


Theoretical massNumber of molelcules
Total (without water)34,6401
Polymers34,6401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dimethyladenosine transferase, putative


Theoretical massNumber of molelcules
Total (without water)34,6401
Polymers34,6401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.008, 82.222, 75.909
Angle α, β, γ (deg.)90.00, 112.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dimethyladenosine transferase, putative


Mass: 34639.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: P28-LIC-THROMBIN DERIVED FROM PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon plus RIL / References: UniProt: Q8ILT8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 23.5% PEG3350, 0.2M Tri Lithium Citrate, 0.1M Hepes at pH7.1, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 7, 2006 / Details: Si(111)
RadiationMonochromator: Si(111) monochromater / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 55385 / Num. obs: 55385 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 9.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 1.95 / Rsym value: 0.474 / % possible all: 87.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCdata collection
HKL-2000data scaling
PHASERV. 1.3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZQ9

1zq9


Resolution: 1.89→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.467 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24954 2825 5.1 %RANDOM
Rwork0.19843 ---
obs0.20111 52513 98.07 %-
all-52513 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.872 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å2-2.08 Å2
2--1.73 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 1.89→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 0 498 4896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224492
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9756080
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6625555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78224.27185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78715840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6741522
X-RAY DIFFRACTIONr_chiral_restr0.1060.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023284
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21976
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23150
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2368
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1561.52866
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81324526
X-RAY DIFFRACTIONr_scbond_it2.94231833
X-RAY DIFFRACTIONr_scangle_it4.4494.51554
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.892→1.941 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 175 -
Rwork0.25 3132 -
obs--79.34 %

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