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- PDB-1ixk: Crystal Structure Analysis of Methyltransferase Homolog Protein f... -

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Basic information

Entry
Database: PDB / ID: 1ixk
TitleCrystal Structure Analysis of Methyltransferase Homolog Protein from Pyrococcus Horikoshii
ComponentsMethyltransferase
KeywordsTRANSFERASE / OPEN BETA SHEET
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / rRNA processing / methylation / RNA binding
Similarity search - Function
Sun protein; domain 3 / Ribosomal RNA small subunit methyltransferase F, N-terminal / N-terminal domain of 16S rRNA methyltransferase RsmF / Nop2p / Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site / NOL1/NOP2/sun family signature. / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. ...Sun protein; domain 3 / Ribosomal RNA small subunit methyltransferase F, N-terminal / N-terminal domain of 16S rRNA methyltransferase RsmF / Nop2p / Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site / NOL1/NOP2/sun family signature. / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / Vaccinia Virus protein VP39 / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
315aa long hypothetical proliferating-cell nucleolar protein p120
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsIshikawa, I. / Sakai, N. / Yao, M. / Watanabe, N. / Tamura, T. / Tanaka, I.
CitationJournal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2004
Title: Crystal structure of human p120 homologue protein PH1374 from Pyrococcus horikoshii
Authors: Ishikawa, I. / Sakai, N. / Tamura, T. / Yao, M. / Watanabe, N. / Tanaka, I.
History
DepositionJun 25, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase


Theoretical massNumber of molelcules
Total (without water)36,2641
Polymers36,2641
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.554, 41.513, 71.065
Angle α, β, γ (deg.)90.00, 114.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methyltransferase /


Mass: 36263.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1374 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star(DE3) / References: UniProt: O50082
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG6000, Citric Acid, Glyserol, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
20.1 Mcitric acid1reservoirpH5.
315 %PEG60001reservoir
41 %1-5 pentandiol1reservoir
55 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9000, 0.9805, 0.9800
DetectorType: MARRESEARCH / Detector: CCD / Date: May 17, 2002
RadiationMonochromator: MIRROR + Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.98051
30.981
ReflectionResolution: 1.9→24 Å / Num. all: 26780 / Num. obs: 26745 / % possible obs: 99 % / Redundancy: 5.7 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.079 / Net I/σ(I): 6.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3875 / Rsym value: 0.271 / % possible all: 98.6
Reflection
*PLUS
Lowest resolution: 23.77 Å / Num. measured all: 152004
Reflection shell
*PLUS
% possible obs: 98.6 % / Rmerge(I) obs: 0.329

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHARPphasing
WARPmodel building
CNSrefinement
CCP4(SCALA)data scaling
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.9→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2663 9.9 %RANDOM
Rwork0.199 ---
all-26754 --
obs-26561 99 %-
Solvent computationSolvent model: throughout / Bsol: 49.4 Å2 / ksol: 0.511 e/Å3
Displacement parametersBiso mean: 22.339 Å2
Baniso -1Baniso -2Baniso -3
1-2.186 Å20 Å20.471 Å2
2---1.069 Å20 Å2
3----1.117 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.258 Å0.215 Å
Luzzati d res low-5 Å
Luzzati sigma a0.173 Å0.104 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2435 0 0 151 2586
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005351
X-RAY DIFFRACTIONc_angle_deg1.20203
X-RAY DIFFRACTIONc_dihedral_angle_d22.52323
X-RAY DIFFRACTIONc_improper_angle_d0.79415
X-RAY DIFFRACTIONc_mcbond_it1.386
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.318
X-RAY DIFFRACTIONc_scangle_it3.414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs
1.9-1.970.2662489.270.22623862634
1.97-2.050.25712620.1972623
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.52323
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79415

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