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- PDB-1dus: MJ0882-A hypothetical protein from M. jannaschii -

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Basic information

Entry
Database: PDB / ID: 1dus
TitleMJ0882-A hypothetical protein from M. jannaschii
ComponentsMJ0882
KeywordsSTRUCTURAL GENOMICS / Hypothetical protein / Methanococcus jannaschii / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


rRNA (guanine-N2-)-methyltransferase activity / rRNA base methylation / Transferases; Transferring one-carbon groups; Methyltransferases
Similarity search - Function
: / Methyltransferase small domain / Methyltransferase small domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable S-adenosylmethionine-dependent methyltransferase MJ0882
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsHung, L. / Huang, L. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2002
Title: Structure-based experimental confirmation of biochemical function to a methyltransferase, MJ0882, from hyperthermophile Methanococcus jannaschii
Authors: Huang, L. / Hung, L. / Odell, M. / Yokota, H. / Kim, R. / Kim, S.H.
History
DepositionJan 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
A: MJ0882


Theoretical massNumber of molelcules
Total (without water)21,9451
Polymers21,9451
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.340, 36.780, 68.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

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Components

#1: Protein MJ0882


Mass: 21945.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: Q58292
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.13
Details: 2.75 M ammonium sulfate, 0.1 M MES, pH 5.13, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mg/mlprotein1drop
250 mmol/LMES1drop
31.375 mol/Lammonium sulfate1drop
40.1 mol/LMES1reservoir
52.75 mol/Lammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9797
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 31, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 23830 / Num. obs: 23819 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 8 % / Rmerge(I) obs: 0.32 / Num. unique all: 1153 / % possible all: 99.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS0.9refinement
RefinementResolution: 1.8→19.57 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 543599.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1609 9.8 %RANDOM
Rwork0.188 ---
all0.192 16808 --
obs0.188 16370 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.36 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20 Å20 Å2
2---0.15 Å20 Å2
3----1.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1534 0 0 163 1697
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it2.432
X-RAY DIFFRACTIONc_mcangle_it3.22.5
X-RAY DIFFRACTIONc_scbond_it3.352
X-RAY DIFFRACTIONc_scangle_it5.012.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.231 253 10 %
Rwork0.173 2270 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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