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- PDB-9jgb: Crystal structure of Nep1 from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 9jgb
TitleCrystal structure of Nep1 from Pyrococcus horikoshii OT3
ComponentsRibosomal RNA small subunit methyltransferase Nep1
KeywordsTRANSFERASE / Conserved arginine residues / Globular loop extension / Inter-subunit interactions / Nep1 / N1-pseudouridine methyltransferase / Trefoil knot
Function / homology
Function and homology information


rRNA (pseudouridine) methyltransferase activity / rRNA base methylation / Transferases; Transferring one-carbon groups; Methyltransferases / rRNA binding
Similarity search - Function
Ribosome biogenesis methyltransferase NEP1, archaea / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / SULFITE ION / Ribosomal RNA small subunit methyltransferase Nep1
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSaha, S. / Kanaujia, S.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR51982/NER/95/2011/2023 India
CitationJournal: Febs J. / Year: 2025
Title: Structural analysis of the ribosome assembly factor Nep1, an N1-specific pseudouridine methyltransferase, reveals mechanistic insights.
Authors: Saha, S. / Kanaujia, S.P.
History
DepositionSep 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)27,2715
Polymers26,9261
Non-polymers3444
Water32418
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)54,54110
Polymers53,8532
Non-polymers6898
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_444x-y-1/3,-y-2/3,-z-2/31
Buried area5110 Å2
ΔGint-35 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.810, 113.810, 102.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ribosomal RNA small subunit methyltransferase Nep1 / 16S rRNA (pseudouridine-N1-)-methyltransferase Nep1


Mass: 26926.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Gene: nep1, PH1379 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta
References: UniProt: O50087, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 5 types, 22 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: Trigonal
Crystal growTemperature: 293 K / Method: microbatch / pH: 8
Details: 0.2M ammonium sulfate, 0.1M Tris-Base pH 8.0, 20% (v/v) PEG smear broad

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 18, 2023 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→71.01 Å / Num. obs: 4773 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.996 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.038 / Rrim(I) all: 0.139 / Χ2: 0.89 / Net I/σ(I): 16.4 / Num. measured all: 62217
Reflection shellResolution: 3.1→3.31 Å / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.427 / Num. measured all: 11144 / Num. unique obs: 847 / CC1/2: 0.955 / Rpim(I) all: 0.122 / Rrim(I) all: 0.445 / Χ2: 0.68 / Net I/σ(I) obs: 5.4

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Processing

Software
NameVersionClassification
HKL-30003000data collection
MOSFLM7.4.0data reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
Coot0.9.4.1model building
PDB_EXTRACT4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→71.01 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.886 / SU B: 36.492 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R Free: 0.503 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24511 251 5.3 %RANDOM
Rwork0.16391 ---
obs0.1683 4521 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.147 Å2
Baniso -1Baniso -2Baniso -3
1--2.31 Å2-1.15 Å20 Å2
2---2.31 Å20 Å2
3---7.49 Å2
Refinement stepCycle: 1 / Resolution: 3.1→71.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1871 0 20 18 1909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0121927
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161912
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.6672595
X-RAY DIFFRACTIONr_angle_other_deg0.3941.5824415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0415225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.829516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65910371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0510.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022185
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02415
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_it1.9172.849903
X-RAY DIFFRACTIONr_mcbond_other1.9162.849903
X-RAY DIFFRACTIONr_mcangle_it3.2835.1091127
X-RAY DIFFRACTIONr_mcangle_other3.2825.1111128
X-RAY DIFFRACTIONr_scbond_it2.2853.2111024
X-RAY DIFFRACTIONr_scbond_other2.2843.2131025
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7625.7491469
X-RAY DIFFRACTIONr_long_range_B_refined7.17327.182140
X-RAY DIFFRACTIONr_long_range_B_other7.17327.192141
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 15 -
Rwork0.128 331 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -2.461 Å / Origin y: -20.5534 Å / Origin z: -32.45 Å
111213212223313233
T0.2515 Å2-0.0204 Å20.0339 Å2-0.2089 Å20.0412 Å2--0.0311 Å2
L3.2408 °20.0995 °20.4647 °2-4.2978 °20.0144 °2--1.0984 °2
S0.1716 Å °-0.1224 Å °0.1766 Å °0.1022 Å °-0.2317 Å °-0.1796 Å °-0.1838 Å °0.0823 Å °0.0602 Å °

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