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- PDB-2oyr: Crystal Structure of UPF0341 Protein (yhiQ) from Shigella flexner... -

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Basic information

Entry
Database: PDB / ID: 2oyr
TitleCrystal Structure of UPF0341 Protein (yhiQ) from Shigella flexneri in complex with S-Adenosyl Homocysteine, Northeast Structural Genomics Target SfR275
ComponentsUPF0341 protein yhiQ
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / 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
S-ADENOSYL-L-HOMOCYSTEINE / Ribosomal RNA small subunit methyltransferase J
Similarity search - Component
Biological speciesShigella flexneri 2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsForouhar, F. / Su, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Baran, M.C. / Liu, J. / Acton, T.B. / Montelione, G.T. ...Forouhar, F. / Su, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Baran, M.C. / Liu, J. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of UPF0341 Protein (yhiQ) from Shigella flexneri in complex with S-Adenosyl Homocysteine, Northeast Structural Genomics Target SfR275
Authors: Forouhar, F. / Su, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Baran, M.C. / Liu, J. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionFeb 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 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 18, 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 yhiQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6932
Polymers28,3091
Non-polymers3841
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.403, 74.737, 79.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UPF0341 protein yhiQ


Mass: 28308.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Species: Shigella flexneri / Strain: 2457T, 301 / Gene: yhiQ, SF3528, S_4240 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7UAV7
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.22 Å3/Da / Density % sol: 44.63 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 8.5
Details: 100mM Tris-HCl pH 8.5, 8% PEG 8000, 50 mM NaCl, 5 mM DTT, 5 mM SAM, MICROBATCH UNDER OIL, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 18, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2→37.41 Å / Num. all: 32699 / Num. obs: 32699 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 5.8 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.064 / Net I/σ(I): 19.81
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 8.51 / Num. unique all: 3288 / Rsym value: 0.246 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
XTALVIEWrefinement
RefinementMethod to determine structure: SAD / Resolution: 2→37.41 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 104483.06 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2946 9.7 %RANDOM
Rwork0.213 ---
all0.214 32699 --
obs0.213 30301 92 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.8131 Å2 / ksol: 0.324387 e/Å3
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.85 Å20 Å20 Å2
2---1.15 Å20 Å2
3----3.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 26 266 2150
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.5
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.235 303 10.4 %
Rwork0.21 2619 -
obs-2619 89.3 %

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