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- PDB-3tpz: 2.1 Angstrom crystal structure of the L114P mutant of E. Coli KsgA -

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Basic information

Entry
Database: PDB / ID: 3tpz
Title2.1 Angstrom crystal structure of the L114P mutant of E. Coli KsgA
ComponentsRibosomal RNA small subunit methyltransferase A
KeywordsTRANSFERASE / rRNA adenine dimethyltransferase / ribogenesis
Function / homology
Function and homology information


16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA base methylation / rRNA methylation / ribosomal small subunit binding / maturation of SSU-rRNA / ribosomal small subunit assembly / rRNA processing / double-stranded DNA binding ...16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA base methylation / rRNA methylation / ribosomal small subunit binding / maturation of SSU-rRNA / ribosomal small subunit assembly / rRNA processing / double-stranded DNA binding / response to antibiotic / mRNA binding / cytosol
Similarity search - Function
rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. ...rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / 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
PHOSPHATE ION / Ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsScarsdale, J.N. / Musayev, F.N. / Rife, J.P.
Citation
Journal: Biochemistry / Year: 2012
Title: Control of Substrate Specificity by a Single Active Site Residue of the KsgA Methyltransferase.
Authors: O'Farrell, H.C. / Musayev, F.N. / Scarsdale, J.N. / Rife, J.P.
#1: Journal: Biochemistry / Year: 2010
Title: Binding of adenosine-based ligands to the MjDim1 rRNA methyltransferase: implications for reaction mechanism and drug design.
Authors: O'Farrell, H.C. / Musayev, F.N. / Scarsdale, J.N. / Rife, J.P.
#2: Journal: J.Mol.Biol. / Year: 2009
Title: Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases.
Authors: Pulicherla, N. / Pogorzala, L.A. / Xu, Z. / O Farrell, H.C. / Musayev, F.N. / Scarsdale, J.N. / Sia, E.A. / Culver, G.M. / Rife, J.P.
#3: Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli.
Authors: O'Farrell, H.C. / Scarsdale, J.N. / Rife, J.P.
History
DepositionSep 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Ribosomal RNA small subunit methyltransferase A
B: Ribosomal RNA small subunit methyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0385
Polymers60,8722
Non-polymers1663
Water3,675204
1
A: Ribosomal RNA small subunit methyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5073
Polymers30,4361
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal RNA small subunit methyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5312
Polymers30,4361
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)239.007, 38.534, 64.752
Angle α, β, γ (deg.)90.00, 96.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribosomal RNA small subunit methyltransferase A / / ecksga / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase / 16S rRNA ...ecksga / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase / 16S rRNA dimethyladenosine transferase / 16S rRNA dimethylase / High level kasugamycin resistance protein ksgA / Kasugamycin dimethyltransferase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase


Mass: 30436.049 Da / Num. of mol.: 2 / Mutation: L114P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0051, JW0050, ksgA, rsmA / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P06992, 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: protein solution: 10 mg/mL ecKsgA, 50 mM Tris, pH 7.4, 50 mM ammonium chloride, 6 mM BME, reservoir solution: 80 mM MES/sodium, pH 6.5, 25% PEG5000 MME, 0.15 M ammonium sulfate , VAPOR ...Details: protein solution: 10 mg/mL ecKsgA, 50 mM Tris, pH 7.4, 50 mM ammonium chloride, 6 mM BME, reservoir solution: 80 mM MES/sodium, pH 6.5, 25% PEG5000 MME, 0.15 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 28, 2008 / Details: Rigaku Varimax Confocal Optics
RadiationMonochromator: Rigaku varimax confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→34.65 Å / Num. all: 34870 / Num. obs: 33415 / % possible obs: 95 % / Redundancy: 3.98 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.95 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 4 / Num. unique all: 3446 / % possible all: 93.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QYR

1qyr


Resolution: 2.1→28 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.913 / SU B: 16.323 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.27566 3339 10 %RANDOM
Rwork0.21145 ---
obs0.21787 30071 95.85 %-
all-34858 --
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: 40.461 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å20.28 Å2
2--0.85 Å20 Å2
3---1.42 Å2
Refine analyzeLuzzati coordinate error obs: 0.348 Å
Refinement stepCycle: LAST / Resolution: 2.1→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 0 7 204 4175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224082
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.9685578
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.575523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13624.611180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52915628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3611522
X-RAY DIFFRACTIONr_chiral_restr0.070.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0223157
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.71742624
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.09284246
X-RAY DIFFRACTIONr_scbond_it6.053121458
X-RAY DIFFRACTIONr_scangle_it8.202151331
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 228 -
Rwork0.354 2169 -
obs--93.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5051-0.3886-0.6560.79020.10910.5256-0.0004-0.15480.05080.05480.1422-0.01620.04990.027-0.14180.16830.0369-0.00760.11560.04470.069776.90044.041416.2595
28.2276-1.2563-1.74970.3740.11130.5205-0.0417-0.84820.83580.00980.138-0.2488-0.03340.1566-0.09630.13620.0165-0.00780.1887-0.05950.2379101.12266.92637.8257
32.0661-0.01690.50791.1776-0.31881.39690.02340.3258-0.1130.0258-0.012-0.0192-0.04590.0787-0.01140.18850.00160.00870.0528-0.01640.008871.8451-1.5178-15.8099
47.68991.22261.09950.4240.04910.2807-0.04860.7165-0.48460.02360.0466-0.25610.03260.19320.0020.12440.0092-0.01450.1612-0.03630.198695.9433-5.0229-7.8682
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 149
2X-RAY DIFFRACTION2A150 - 267
3X-RAY DIFFRACTION3B15 - 149
4X-RAY DIFFRACTION4B150 - 267

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