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- PDB-3b89: Crystal structure of rRNA methylase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 3b89
TitleCrystal structure of rRNA methylase from Escherichia coli
Components16S rRNA methylase
KeywordsTRANSFERASE / 10094b / NYSGXRC / rmtB / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / Methyltransferase / Plasmid
Function / homology
Function and homology information


16S rRNA (guanine1405-N7)-methyltransferase / rRNA methyltransferase activity / response to antibiotic
Similarity search - Function
Ribosomal RNA aminoglycoside-resistance methyltransferase, Gram-negative bacteria / Ribosomal RNA aminoglycoside-resistance methyltransferase / Ribosomal RNA methyltransferase (FmrO) / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Ribosomal RNA aminoglycoside-resistance methyltransferase, Gram-negative bacteria / Ribosomal RNA aminoglycoside-resistance methyltransferase / Ribosomal RNA methyltransferase (FmrO) / Ubiquitin-associated (UBA) domain / 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
GUANOSINE-5'-MONOPHOSPHATE / 16S rRNA (guanine(1405)-N(7))-methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsEswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of rRNA methylase from Escherichia coli.
Authors: Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionOct 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: 16S rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0152
Polymers27,6511
Non-polymers3631
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.262, 94.131, 96.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein 16S rRNA methylase / 16S ribosomal RNA methylase


Mass: 27651.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rmtB / Production host: Escherichia coli (E. coli) / References: UniProt: Q763K9
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris, 28% PEG MME 2000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 7962 / Num. obs: 7962 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.282 / Num. unique all: 673 / % possible all: 83.8

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.2824 745 -RANDOM
Rwork0.2265 ---
all0.266 7746 --
obs-7746 94.9 %-
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1--8.55 Å20 Å20 Å2
2--3.01 Å20 Å2
3---5.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1843 0 24 40 1907
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_deg0.94
LS refinement shellResolution: 2.6→2.76 Å
RfactorNum. reflection% reflection
Rfree0.328 94 -
Rwork0.316 --
obs-934 78.4 %

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