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- PDB-4xcx: METHYLTRANSFERASE DOMAIN OF SMALL RNA 2'-O-METHYLTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 4xcx
TitleMETHYLTRANSFERASE DOMAIN OF SMALL RNA 2'-O-METHYLTRANSFERASE
ComponentsSmall RNA 2'-O-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / SAH / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


small RNA 2'-O-methyltransferase activity / small RNA 2'-O-methyltransferase / piRNA processing / RNA methyltransferase activity / RNA methylation / siRNA processing / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / P granule / PIWI-interacting RNA (piRNA) biogenesis ...small RNA 2'-O-methyltransferase activity / small RNA 2'-O-methyltransferase / piRNA processing / RNA methyltransferase activity / RNA methylation / siRNA processing / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / P granule / PIWI-interacting RNA (piRNA) biogenesis / RNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
3'-RNA ribose 2'-O-methyltransferase, Hen1 / 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 / Small RNA 2'-O-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsWalker, J.R. / Zeng, H. / Dong, A. / Li, Y. / Wernimont, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Crystal structure of human C1ORF59 in complex with SAH
Authors: Walker, J.R. / Zeng, H. / Dong, A. / Li, Y. / Wernimont, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC)
History
DepositionDec 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Jan 24, 2018Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / entity_src_gen / pdbx_struct_oper_list
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small RNA 2'-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7312
Polymers28,3471
Non-polymers3841
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.025, 166.025, 74.478
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Detailsbiological unit is the same as asym.

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Components

#1: Protein Small RNA 2'-O-methyltransferase / HEN1 methyltransferase homolog 1


Mass: 28347.062 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 14-262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HENMT1, C1orf59 / Plasmid: PET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus RIL
References: UniProt: Q5T8I9, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 5.21 Å3/Da / Density % sol: 76.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 2.4 M NACL, 0.1 M TRIS-HCL, PH 8.6,4% 1,3-PROPANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.84→35 Å / Num. obs: 14604 / % possible obs: 98.4 % / Redundancy: 12.3 % / Biso Wilson estimate: 80.33 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.028 / Rrim(I) all: 0.103 / Χ2: 1.095 / Net I/av σ(I): 24.25 / Net I/σ(I): 24.25 / Num. measured all: 180091
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.84-2.9411.70.7312.0813920.8820.2090.7630.82495.7
2.94-3.0612.30.57714120.9340.1650.6020.85398.1
3.06-3.212.60.40314440.9620.1150.420.85399
3.2-3.3712.70.26814360.9870.0760.280.87699.4
3.37-3.5812.70.20314580.9930.0580.2121.01799.1
3.58-3.8512.70.12414530.9960.0350.1291.08699.5
3.85-4.2412.60.09414610.9980.0270.0981.12798.9
4.24-4.8512.50.06714690.9990.0190.0691.3498.9
4.85-6.1112.20.07415030.9980.0210.0771.70498.6
6.11-3511.50.03915760.9990.0110.041.2297

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Processing

Software
NameVersionClassification
HKL-3000data reduction
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JWG

3jwg


Resolution: 2.84→33.98 Å / Cor.coef. Fo:Fc: 0.8825 / Cor.coef. Fo:Fc free: 0.8796 / SU R Cruickshank DPI: 0.726 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.306 / SU Rfree Blow DPI: 0.243 / SU Rfree Cruickshank DPI: 0.245
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 737 5.07 %RANDOM
Rwork0.2251 ---
obs0.2263 14545 98.54 %-
Displacement parametersBiso max: 186.82 Å2 / Biso mean: 93.03 Å2 / Biso min: 57.87 Å2
Baniso -1Baniso -2Baniso -3
1-25.7195 Å20 Å20 Å2
2--25.7195 Å20 Å2
3----51.439 Å2
Refine analyzeLuzzati coordinate error obs: 0.575 Å
Refinement stepCycle: final / Resolution: 2.84→33.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 26 17 1733
Biso mean--85.89 70.77 -
Num. residues----216
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d705SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes503HARMONIC5
X-RAY DIFFRACTIONt_it3326HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion227SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3650SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3326HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5968HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion17.53
LS refinement shellResolution: 2.84→3.07 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2934 138 4.79 %
Rwork0.2623 2746 -
all0.2639 2884 -
obs--98.54 %
Refinement TLS params.Method: refined / Origin x: 33.9105 Å / Origin y: 98.0601 Å / Origin z: 9.4459 Å
111213212223313233
T0.3035 Å20.075 Å20.2321 Å2-0.2376 Å2-0.2504 Å2--0.6827 Å2
L3.3923 °2-0.5618 °2-0.8275 °2-2.2629 °2-0.4357 °2--1.8037 °2
S0.1763 Å °0.242 Å °0.302 Å °-0.291 Å °0.152 Å °-0.7905 Å °-0.1389 Å °-0.0008 Å °-0.3283 Å °
Refinement TLS groupSelection details: { A|26 - A|400 }

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