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- PDB-7d8f: The crystal structure of ScNTM1 in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 7d8f
TitleThe crystal structure of ScNTM1 in complex with SAH
ComponentsAlpha N-terminal protein methyltransferase 1
KeywordsTRANSFERASE / ScNTM1 / N-terminal methylation / methyltransferase / Saccharomyces cerevisiae / substrate binding pocket
Function / homology
Function and homology information


protein N-terminal methyltransferase / N-terminal protein N-methyltransferase activity / methylation / cytoplasmic translation / cytoplasm / cytosol
Similarity search - Function
Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Alpha N-terminal protein methyltransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsZhang, H.Y. / Yue, J. / Zhu, Z.L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U1632124 to L.N., 31270770 China
Ministry of Science and Technology (MoST, China)2017YFA0503600 to L.N China
CitationJournal: Crystallography Reports / Year: 2021
Title: Structural Basis for Peptide Binding of Alpha-N Terminal Methyltransferase from Saccharomyces cerevisiae
Authors: Zhang, H.Y. / Kuang, Z. / Xue, L. / Yue, J. / Khan, M.H. / Zhu, Z. / Niu, L.
History
DepositionOct 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author / database_2
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.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7592
Polymers26,3751
Non-polymers3841
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10960 Å2
Unit cell
Length a, b, c (Å)38.402, 52.148, 120.017
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Alpha N-terminal protein methyltransferase 1 / Translation associated element 1 / X-Pro-Lys N-terminal protein methyltransferase 1 / NTM1


Mass: 26375.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TAE1, NTM1, YBR261C, YBR1729 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P38340, protein N-terminal methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 46.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.8M sodium acetate trihydrate pH 7.0, 3.5M sodium formate pH 7.0, 20% PEG3350,0.2M magnesium nitrate hexahydrate
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97853 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 88586 / % possible obs: 89.7 % / Redundancy: 12.8 % / Biso Wilson estimate: 10.4 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.018 / Rrim(I) all: 0.064 / Net I/σ(I): 28.6
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 3.3 % / Num. unique obs: 2039 / CC1/2: 0.559 / % possible all: 42

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Processing

Software
NameVersionClassification
HKL-20001.18.2_3874data collection
PHENIX1.18.2_3874refinement
HKL-20001.10.1_2155data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EX4

2ex4


Resolution: 1.15→23.91 Å / SU ML: 0.0769 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.3207
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1398 4155 5.03 %
Rwork0.1221 78381 -
obs0.123 82645 95.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.96 Å2
Refinement stepCycle: LAST / Resolution: 1.15→23.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 26 269 2146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691981
X-RAY DIFFRACTIONf_angle_d1.05822703
X-RAY DIFFRACTIONf_chiral_restr0.0807296
X-RAY DIFFRACTIONf_plane_restr0.0072351
X-RAY DIFFRACTIONf_dihedral_angle_d19.8728762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.170.22321260.19762618X-RAY DIFFRACTION63.93
1.17-1.190.19081320.17052953X-RAY DIFFRACTION72.78
1.19-1.210.16181880.14253273X-RAY DIFFRACTION80.69
1.21-1.240.15621940.12433677X-RAY DIFFRACTION89.92
1.24-1.270.12652160.11273993X-RAY DIFFRACTION99.53
1.27-1.30.12992110.10784065X-RAY DIFFRACTION100
1.3-1.330.13862050.10194104X-RAY DIFFRACTION100
1.33-1.360.13712180.10284053X-RAY DIFFRACTION100
1.36-1.40.1342050.10844089X-RAY DIFFRACTION100
1.4-1.450.13572230.10984074X-RAY DIFFRACTION100
1.45-1.50.13342430.10354067X-RAY DIFFRACTION100
1.5-1.560.11511870.09894084X-RAY DIFFRACTION100
1.56-1.630.12692020.10064127X-RAY DIFFRACTION99.98
1.63-1.720.13022480.10434063X-RAY DIFFRACTION99.98
1.72-1.830.11552120.11244125X-RAY DIFFRACTION100
1.83-1.970.14362480.11454093X-RAY DIFFRACTION99.98
1.97-2.160.12182220.11084152X-RAY DIFFRACTION99.95
2.16-2.480.13552190.11794161X-RAY DIFFRACTION100
2.48-3.120.14512110.13044220X-RAY DIFFRACTION100
3.12-23.910.15752450.14674390X-RAY DIFFRACTION99.94

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