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- PDB-5fai: EMG1 N1-Specific Pseudouridine Methyltransferase -

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Basic information

Entry
Database: PDB / ID: 5fai
TitleEMG1 N1-Specific Pseudouridine Methyltransferase
ComponentsRibosomal RNA small subunit methyltransferase NEP1
KeywordsTRANSFERASE / EMG1 / Methyltransferase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


nucleologenesis / rRNA (pseudouridine) methyltransferase activity / rRNA base methylation / rRNA modification in the nucleus and cytosol / blastocyst development / Major pathway of rRNA processing in the nucleolus and cytosol / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / ribosomal small subunit biogenesis / rRNA processing ...nucleologenesis / rRNA (pseudouridine) methyltransferase activity / rRNA base methylation / rRNA modification in the nucleus and cytosol / blastocyst development / Major pathway of rRNA processing in the nucleolus and cytosol / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / ribosomal small subunit biogenesis / rRNA processing / chromosome / rRNA binding / nucleolus / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / S-ADENOSYL-L-HOMOCYSTEINE / Ribosomal RNA small subunit methyltransferase NEP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsDONG, A. / ZENG, H. / LI, Y. / TEMPEL, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: EMG1 N1-Specific Pseudouridine Methyltransferase
Authors: ZENG, H. / DONG, A. / LI, Y. / TEMPEL, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC)
History
DepositionDec 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal RNA small subunit methyltransferase NEP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,13616
Polymers25,3681
Non-polymers76915
Water2,846158
1
A: Ribosomal RNA small subunit methyltransferase NEP1
hetero molecules

A: Ribosomal RNA small subunit methyltransferase NEP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,27232
Polymers50,7352
Non-polymers1,53730
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area4280 Å2
ΔGint-3 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.118, 86.118, 125.178
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-465-

HOH

21A-534-

HOH

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Components

#1: Protein Ribosomal RNA small subunit methyltransferase NEP1 / / 18S rRNA (pseudouridine(1248)-N1)-methyltransferase / 18S rRNA Psi1248 methyltransferase / ...18S rRNA (pseudouridine(1248)-N1)-methyltransferase / 18S rRNA Psi1248 methyltransferase / Nucleolar protein EMG1 homolog / Protein C2f / Ribosome biogenesis protein NEP1


Mass: 25367.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMG1, C2F / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus RIL
References: UniProt: Q92979, Transferases; Transferring one-carbon groups; Methyltransferases
#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: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M di-NH4 Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 26058 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Χ2: 1.294 / Net I/av σ(I): 26.862 / Net I/σ(I): 8.4 / Num. measured all: 181554
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.837.10.91212700.80.3630.9820.954100
1.83-1.867.10.78412710.8320.3130.8450.956100
1.86-1.97.10.66212650.880.2640.7140.997100
1.9-1.947.10.5412610.9210.2150.5821.019100
1.94-1.987.10.44712790.9320.1780.4821.042100
1.98-2.037.10.36612910.9620.1460.3941.057100
2.03-2.087.10.312750.9710.120.3231.097100
2.08-2.137.10.23912770.9780.0950.2581.095100
2.13-2.27.10.21812840.9780.0870.2351.128100
2.2-2.277.10.18712850.9870.0750.2011.106100
2.27-2.357.10.15212820.9930.0610.1641.117100
2.35-2.447.10.13712920.9930.0550.1481.163100
2.44-2.557.10.11912920.9930.0480.1281.186100
2.55-2.6970.113000.9960.040.1081.154100
2.69-2.8670.09113110.9960.0360.0981.311100
2.86-3.0870.07813130.9960.0320.0841.734100
3.08-3.396.80.06713210.9970.0280.0722.345100
3.39-3.886.70.05913350.9970.0240.0642.682100
3.88-4.886.60.03613660.9990.0150.0391.532100
4.88-506.30.03114880.9990.0130.0341.25899.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.85 Å64.02 Å
Translation1.85 Å64.02 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.7phasing
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V3K

2v3k


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.208 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1833 807 3.1 %RANDOM
Rwork0.168 ---
obs0.1684 25185 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.44 Å2 / Biso mean: 23.676 Å2 / Biso min: 13.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.23 Å20 Å2
2--0.47 Å20 Å2
3----1.51 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1589 0 85 162 1836
Biso mean--27.6 34.68 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191808
X-RAY DIFFRACTIONr_bond_other_d0.0020.021744
X-RAY DIFFRACTIONr_angle_refined_deg1.412.0182481
X-RAY DIFFRACTIONr_angle_other_deg0.73934024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7275234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82823.63666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7915301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3921514
X-RAY DIFFRACTIONr_chiral_restr0.2820.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212058
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02386
X-RAY DIFFRACTIONr_mcbond_it1.4592.229900
X-RAY DIFFRACTIONr_mcbond_other1.4572.23898
X-RAY DIFFRACTIONr_mcangle_it2.2773.3361137
LS refinement shellResolution: 1.802→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 50 -
Rwork0.236 1805 -
all-1855 -
obs--99.25 %

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