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- PDB-6dub: Crystal structure of a methyltransferase -

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Basic information

Entry
Database: PDB / ID: 6dub
TitleCrystal structure of a methyltransferase
Components
  • Alpha N-terminal protein methyltransferase 1B
  • RCC1
KeywordsTRANSFERASE / methyltransferase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


protein N-terminal monomethyltransferase / N-terminal protein amino acid methylation / N-terminal protein N-methyltransferase activity / mitotic nuclear membrane reassembly / sulfate binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / regulation of mitotic nuclear division / spindle assembly ...protein N-terminal monomethyltransferase / N-terminal protein amino acid methylation / N-terminal protein N-methyltransferase activity / mitotic nuclear membrane reassembly / sulfate binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / Postmitotic nuclear pore complex (NPC) reformation / regulation of mitotic nuclear division / spindle assembly / nucleosome binding / nucleosomal DNA binding / viral process / guanyl-nucleotide exchange factor activity / mitotic spindle organization / condensed nuclear chromosome / chromosome segregation / small GTPase binding / G1/S transition of mitotic cell cycle / chromosome / histone binding / protein heterodimerization activity / cell division / chromatin binding / chromatin / protein-containing complex / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Regulator of chromosome condensation (RCC1) signature 1. / Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Regulator of chromosome condensation (RCC1) signature 1. / Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / 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 / Regulator of chromosome condensation / N-terminal Xaa-Pro-Lys N-methyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsDong, C. / Tempel, W. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Commun Biol / Year: 2018
Title: An asparagine/glycine switch governs product specificity of human N-terminal methyltransferase NTMT2.
Authors: Dong, C. / Dong, G. / Li, L. / Zhu, L. / Tempel, W. / Liu, Y. / Huang, R. / Min, J.
History
DepositionJun 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Alpha N-terminal protein methyltransferase 1B
B: Alpha N-terminal protein methyltransferase 1B
E: RCC1
F: RCC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,43069
Polymers51,3854
Non-polymers1,04565
Water5,657314
1
A: Alpha N-terminal protein methyltransferase 1B
E: RCC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,26142
Polymers25,6932
Non-polymers56940
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-5 kcal/mol
Surface area10440 Å2
MethodPISA
2
B: Alpha N-terminal protein methyltransferase 1B
F: RCC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,16927
Polymers25,6932
Non-polymers47725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-4 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.359, 44.359, 262.058
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABEF

#1: Protein Alpha N-terminal protein methyltransferase 1B / Methyltransferase-like protein 11B / X-Pro-Lys N-terminal protein methyltransferase 1B / NTM1B


Mass: 25005.688 Da / Num. of mol.: 2 / Fragment: UNP residues 58-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL11B, C1orf184, NRMT2 / Plasmid: pET28-MKH8SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-V3R
References: UniProt: Q5VVY1, protein N-terminal monomethyltransferase
#2: Protein/peptide RCC1


Mass: 686.843 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P18754*PLUS

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Non-polymers , 4 types, 379 molecules

#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 60 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 30% PEG2000, 0.1 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 23, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.2→31.14 Å / Num. obs: 150535 / % possible obs: 96 % / Redundancy: 6.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Net I/σ(I): 11 / Num. measured all: 914436 / Scaling rejects: 235
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.2-1.226.60.9734742371910.6750.4041.056293.2
6.57-31.146.90.06267339820.9950.0260.06732.199

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
Aimless0.5.21data scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5E1D

5e1d


Resolution: 1.2→31.1 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.144 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.1778 4983 3.3 %
Rwork0.154 --
obs0.1548 145394 95.91 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.51 Å2 / Biso mean: 16.091 Å2 / Biso min: 5.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.71 Å2
Refinement stepCycle: final / Resolution: 1.2→31.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3509 0 154 314 3977
Biso mean--18.81 25.77 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193888
X-RAY DIFFRACTIONr_bond_other_d0.0010.023687
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.9985291
X-RAY DIFFRACTIONr_angle_other_deg0.92138584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1765506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41223.494166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49315692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0891530
X-RAY DIFFRACTIONr_chiral_restr0.120.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214303
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02806
X-RAY DIFFRACTIONr_mcbond_it2.0241.4581883
X-RAY DIFFRACTIONr_mcbond_other2.0241.4581884
X-RAY DIFFRACTIONr_mcangle_it2.7062.2082361
X-RAY DIFFRACTIONr_rigid_bond_restr2.737574
X-RAY DIFFRACTIONr_sphericity_free18.0255223
X-RAY DIFFRACTIONr_sphericity_bonded8.28257623
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.225 10825 -
obs--93.16 %

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