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- PDB-2r6z: Crystal structure of the SAM-dependent methyltransferase NGO1261 ... -

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Basic information

Entry
Database: PDB / ID: 2r6z
TitleCrystal structure of the SAM-dependent methyltransferase NGO1261 from Neisseria gonorrhoeae, Northeast Structural Genomics Consortium Target NgR48
ComponentsUPF0341 protein in rsp 3' region
KeywordsTRANSFERASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


16S rRNA (guanine1516-N2)-methyltransferase / rRNA (guanine-N2-)-methyltransferase activity / cytoplasm
Similarity search - Function
S-adenosyl-L-methionine-dependent methyltransferases / YhiQ-like domain / Ribosomal RNA small subunit methyltransferase J / Putative SAM-dependent methyltransferase / 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 small subunit methyltransferase J
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsForouhar, F. / Abashidze, M. / Seetharaman, J. / Mao, L. / Nwosu, C. / Fang, Y. / Xiao, R. / Baran, M.C. / Acton, T.B. / Montelione, G.T. ...Forouhar, F. / Abashidze, M. / Seetharaman, J. / Mao, L. / Nwosu, C. / Fang, Y. / Xiao, R. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the SAM-dependent methyltransferase NGO1261 from Neisseria gonorrhoeae.
Authors: Forouhar, F. / Abashidze, M. / Seetharaman, J. / Mao, L. / Nwosu, C. / Fang, Y. / Xiao, R. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
History
DepositionSep 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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: UPF0341 protein in rsp 3' region
B: UPF0341 protein in rsp 3' region


Theoretical massNumber of molelcules
Total (without water)57,2262
Polymers57,2262
Non-polymers00
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.233, 43.186, 103.570
Angle α, β, γ (deg.)90.00, 97.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UPF0341 protein in rsp 3' region


Mass: 28612.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: MS11, FA 1090 / Gene: NGO1261 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P72077
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 6.5
Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM DTT. Reservoir solution: 100 mM Cacodylic acid pH 6.5, 18% PEG 3350, MICROBATCH UNDER OIL, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97893 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 29, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.8→26.82 Å / Num. all: 91274 / Num. obs: 91274 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.031 / Net I/σ(I): 28.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.96 / Num. unique all: 8942 / Rsym value: 0.27 / % possible all: 96.6

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→26.82 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 513500.77 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used for phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.231 7737 9.8 %RANDOM
Rwork0.215 ---
all0.216 91274 --
obs0.215 79216 85.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.7004 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--2.87 Å20 Å22.95 Å2
2--4.53 Å20 Å2
3----1.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8→26.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3598 0 0 453 4051
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.279 461 9 %
Rwork0.239 4635 -
obs-4635 55.1 %

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