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- PDB-2oo3: Crystal structure of protein LPL1258 from Legionella pneumophila ... -

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Basic information

Entry
Database: PDB / ID: 2oo3
TitleCrystal structure of protein LPL1258 from Legionella pneumophila str. Philadelphia 1, Pfam DUF519
ComponentsProtein involved in catabolism of external DNA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


23S rRNA (adenine2030-N6)-methyltransferase / 23S rRNA (adenine(2030)-N(6))-methyltransferase activity / rRNA base methylation / RNA binding
Similarity search - Function
Ribosomal RNA large subunit methyltransferase J / Ribosomal RNA large subunit methyltransferase D, RlmJ / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA large subunit methyltransferase J
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBonanno, J.B. / Freeman, J. / Bain, K.T. / Slocombe, A. / Reyes, C. / Ozyurt, S. / Smyth, L. / Atwell, S. / Sauder, J.M. / Burley, S.K. ...Bonanno, J.B. / Freeman, J. / Bain, K.T. / Slocombe, A. / Reyes, C. / Ozyurt, S. / Smyth, L. / Atwell, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of the hypothetical lpl1258 protein from Legionella pneumophila
Authors: Bonanno, J.B. / Freeman, J. / Bain, K.T. / Slocombe, A. / Reyes, C. / Ozyurt, S. / Smyth, L. / Atwell, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJan 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Structure summary
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Dec 27, 2023Group: 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: Protein involved in catabolism of external DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2634
Polymers32,9751
Non-polymers2883
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.822, 72.959, 78.379
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsprobable monomer

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Components

#1: Protein Protein involved in catabolism of external DNA


Mass: 32974.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Species: Legionella pneumophila / Strain: lens, Philadelphia 1 / Gene: lpl1258, lpg1296, DSM 7513 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZVZ2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 1.99 Å3/Da / Density % sol: 38.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: 100mM Bis-Tris pH 6.5, 25% PEG 3350, 200mM Ammonium sulfate, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97958 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 20, 2007
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2→53.4 Å / Num. obs: 18365 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 21.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 9.4 / Num. measured all: 21219 / Num. unique all: 2619 / Rsym value: 0.187 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.368 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.183 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21 941 5.1 %RANDOM
Rwork0.164 ---
obs0.166 18343 99.9 %-
all-18361 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.162 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å20 Å2
2---0.81 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 15 163 2374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222280
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9823101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5825269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55723.762101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81515396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4611510
X-RAY DIFFRACTIONr_chiral_restr0.10.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021707
X-RAY DIFFRACTIONr_nbd_refined0.2050.21040
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21552
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2140
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.225
X-RAY DIFFRACTIONr_mcbond_it1.0331.51380
X-RAY DIFFRACTIONr_mcangle_it1.70422195
X-RAY DIFFRACTIONr_scbond_it2.74831042
X-RAY DIFFRACTIONr_scangle_it4.0164.5904
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 57 -
Rwork0.167 1250 -
obs-1307 98.72 %

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