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- PDB-1p91: Crystal Structure of RlmA(I) enzyme: 23S rRNA n1-G745 methyltrans... -

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Basic information

Entry
Database: PDB / ID: 1p91
TitleCrystal Structure of RlmA(I) enzyme: 23S rRNA n1-G745 methyltransferase (NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER19)
ComponentsRibosomal RNA large subunit methyltransferase A
KeywordsTRANSFERASE / RlmA / RrmA / methyltransferase / G745 / ER19 / 23S rRNA / NESG / STRUCTURAL GENOMICS / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


23S rRNA (guanine745-N1)-methyltransferase / 23S rRNA (guanine(745)-N(1))-methyltransferase activity / rRNA (guanine-N1-)-methyltransferase activity / rRNA base methylation / methyltransferase activity / zinc ion binding
Similarity search - Function
rRNA (guanine-N1-)-methyltransferase A, predicted / Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / 23S rRNA (guanine(745)-N(1))-methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsDas, K. / Acton, T. / Montelione, G. / Arnold, E. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site.
Authors: Das, K. / Acton, T. / Chiang, Y. / Shih, L. / Arnold, E. / Montelione, G.T.
History
DepositionMay 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal RNA large subunit methyltransferase A
B: Ribosomal RNA large subunit methyltransferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,98411
Polymers61,5762
Non-polymers1,4089
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.187, 122.279, 143.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a dimer. One monomers is related to the other by ~159 degree rotation about the NCS axis.

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Components

#1: Protein Ribosomal RNA large subunit methyltransferase A / / rRNA (guanine-N(1)-)-methyltransferase / 23S rRNA n1-G745 methyltransferase


Mass: 30788.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RRMA OR B1822 / Production host: Escherichia coli (E. coli) / References: UniProt: P36999, EC: 2.1.1.51
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.81 Å3/Da / Density % sol: 67.68 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 6.5
Details: Ammonium sulfate, Lithium Sulfate, pH 6.5, VAPOR DIFFUSION, temperature 300K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
35 mMSAM1drop
45 mMdithiothreitol1drop
50.5 Mammonium sulfate1reservoir
61.0 Mlithium sulfate1reservoir
70.1 Msodium citrate1reservoirpH6.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11051
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12C10.97889, 0.97874, 0.9500
SYNCHROTRONCHESS F120.916
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDOct 1, 2002
ADSC QUANTUM 42CCDNov 1, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978891
20.978741
30.951
40.9161
ReflectionResolution: 2.8→50 Å / Num. all: 21876 / Num. obs: 21876 / % possible obs: 93 % / Observed criterion σ(I): -0.5 / Biso Wilson estimate: 41.8 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 11
Reflection shellResolution: 2.8→2.85 Å / % possible all: 80.2
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 93 % / Num. measured all: 88268

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2974439.24 / Data cutoff high rms absF: 2974439.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1138 5.2 %RANDOM
Rwork0.248 ---
all0.248 ---
obs0.248 21804 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.251692 e/Å3
Displacement parametersBiso mean: 55.8 Å2
Baniso -1Baniso -2Baniso -3
1--19.33 Å20 Å20 Å2
2---9.08 Å20 Å2
3---28.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.99 Å0.95 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 81 85 4342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d1.27
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.449 168 5.3 %
Rwork0.429 3019 -
obs-3187 83 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2ION.PARAM&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3SAM.PAR&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4WATER_REP.PARAM&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5SO4.PAR&_1_TOPOLOGY_INFILE_5
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.27

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