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- PDB-6pva: The structure of NTMT1 in complex with compound 11 -

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Basic information

Entry
Database: PDB / ID: 6pva
TitleThe structure of NTMT1 in complex with compound 11
Components
  • AMINO GROUP-()-LYSINE-()-LYSINE-()-PROLINE-()-AMINO-ACETALDEHYDE-()-5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine
  • N-terminal Xaa-Pro-Lys N-methyltransferase 1
Keywordstransferase/transferase inhibitor / methyltransferase / enzyme / inhibitor complex / TRANSFERASE / transferase-transferase inhibitor complex
Function / homology
Function and homology information


N-terminal peptidyl-glycine methylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal peptidyl-proline dimethylation / N-terminal protein N-methyltransferase activity / protein methyltransferase activity / spindle organization / histone methyltransferase activity / chromosome segregation ...N-terminal peptidyl-glycine methylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal peptidyl-proline dimethylation / N-terminal protein N-methyltransferase activity / protein methyltransferase activity / spindle organization / histone methyltransferase activity / chromosome segregation / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
N-terminal Xaa-Pro-Lys N-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsNoinaj, N. / Chen, D. / Huang, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1U01CA214649-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM117275-01A1 United States
CitationJournal: To Be published
Title: The structure of NTMT1 in complex with compound 11
Authors: Chen, D. / Noinaj, N. / Huang, R.
History
DepositionJul 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _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 1.3Oct 11, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
A: AMINO GROUP-()-LYSINE-()-LYSINE-()-PROLINE-()-AMINO-ACETALDEHYDE-()-5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine


Theoretical massNumber of molelcules
Total (without water)28,1392
Polymers28,1392
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-3 kcal/mol
Surface area10190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.012, 73.012, 82.172
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-393-

HOH

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Components

#1: Protein N-terminal Xaa-Pro-Lys N-methyltransferase 1 / Alpha N-terminal protein methyltransferase 1A / Methyltransferase-like protein 11A / N-terminal ...Alpha N-terminal protein methyltransferase 1A / Methyltransferase-like protein 11A / N-terminal RCC1 methyltransferase / X-Pro-Lys N-terminal protein methyltransferase 1A / NTM1A


Mass: 27320.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTMT1, C9orf32, METTL11A, NRMT, NRMT1, AD-003 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9BV86, protein N-terminal methyltransferase
#2: Protein/peptide AMINO GROUP-()-LYSINE-()-LYSINE-()-PROLINE-()-AMINO-ACETALDEHYDE-()-5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine


Mass: 818.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.5 M lithium sulfate; 0.1 M sodium HEPES 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.84→30 Å / Num. obs: 22463 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 35.45 Å2 / CC1/2: 1 / Rsym value: 0.12 / Net I/σ(I): 9.9
Reflection shellResolution: 1.84→1.89 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1586 / CC1/2: 0.14 / Rsym value: 3.3 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DTN

6dtn


Resolution: 1.84→29.51 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 1970 8.82 %
Rwork0.1958 20360 -
obs0.199 22330 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.88 Å2 / Biso mean: 38.0236 Å2 / Biso min: 21.11 Å2
Refinement stepCycle: final / Resolution: 1.84→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1777 0 59 154 1990
Biso mean--34.96 41.98 -
Num. residues----225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.890.38471280.3971340146893
1.89-1.940.39051370.354114261563100
1.94-1.990.30661420.311614501592100
1.99-2.060.33731400.271614291569100
2.06-2.130.30461380.264814431581100
2.13-2.220.26061430.227914581601100
2.22-2.320.281420.224414231565100
2.32-2.440.30011440.212914851629100
2.44-2.590.26771420.226314331575100
2.59-2.790.24571410.196414681609100
2.79-3.070.22761400.20114611601100
3.07-3.520.21911390.169514771616100
3.52-4.430.16681400.158615001640100
4.43-29.510.19761540.1615671721100

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