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- PDB-2ha8: Methyltransferase Domain of Human TAR (HIV-1) RNA binding protein 1 -

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Basic information

Entry
Database: PDB / ID: 2ha8
TitleMethyltransferase Domain of Human TAR (HIV-1) RNA binding protein 1
ComponentsTAR (HIV-1) RNA loop binding protein
KeywordsRNA BINDING PROTEIN / Methyltransferase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


tRNA (guanine) methyltransferase activity / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of transcription by RNA polymerase II / RNA binding / nucleus
Similarity search - Function
Probable methyltransferase TARBP1 / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Armadillo-type fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Probable methyltransferase TARBP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMin, J. / Wu, H. / Zeng, H. / Loppnau, P. / Battaile, K. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Min, J. / Wu, H. / Zeng, H. / Loppnau, P. / Battaile, K. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of Methyltransferase Domain of Human TAR (HIV-1) RNA binding protein 1 in complex with S-adenosyl-L-homocystein.
Authors: Wu, H. / Min, J. / Zeng, H. / Loppnau, P. / Battaile, K. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionJun 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TAR (HIV-1) RNA loop binding protein
B: TAR (HIV-1) RNA loop binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6564
Polymers40,8872
Non-polymers7692
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-20 kcal/mol
Surface area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.237, 86.930, 48.266
Angle α, β, γ (deg.)90.00, 100.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TAR (HIV-1) RNA loop binding protein / TAR HIV-1 / RNA binding protein 1


Mass: 20443.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRP-185 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13395
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 5kMME, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2006
RadiationMonochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→47.4 Å / Num. all: 42523 / Num. obs: 42523 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.6→1.64 Å / % possible all: 67.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→47.4 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.622 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20882 2133 5 %RANDOM
Rwork0.17684 ---
obs0.17839 40358 96.4 %-
all-40358 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.752 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0.39 Å2
2--1.16 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2462 0 52 308 2822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222561
X-RAY DIFFRACTIONr_angle_refined_deg1.3852.013490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.415319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91425.743101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21715458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5371510
X-RAY DIFFRACTIONr_chiral_restr0.090.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021860
X-RAY DIFFRACTIONr_nbd_refined0.2090.21229
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21761
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.226
X-RAY DIFFRACTIONr_mcbond_it0.9151.51635
X-RAY DIFFRACTIONr_mcangle_it1.55822589
X-RAY DIFFRACTIONr_scbond_it2.44231053
X-RAY DIFFRACTIONr_scangle_it3.9214.5901
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 97 -
Rwork0.247 2066 -
obs--66.9 %

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