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- PDB-5ubb: Crystal structure of human alpha N-terminal protein methyltransfe... -

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Basic information

Entry
Database: PDB / ID: 5ubb
TitleCrystal structure of human alpha N-terminal protein methyltransferase 1B
ComponentsAlpha N-terminal protein methyltransferase 1B
KeywordsTRANSFERASE / methyl transferase / 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 / nucleus / cytoplasm
Similarity search - Function
Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / N-terminal Xaa-Pro-Lys N-methyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDong, C. / Zhu, L. / Tempel, W. / Dong, A. / 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
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Alpha N-terminal protein methyltransferase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,40428
Polymers25,0061
Non-polymers39827
Water1,13563
1
A: Alpha N-terminal protein methyltransferase 1B
hetero molecules

A: Alpha N-terminal protein methyltransferase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,80856
Polymers50,0112
Non-polymers79754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_275-x-3,-y+2,z1
Buried area1520 Å2
ΔGint-9 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.595, 132.962, 42.292
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-429-

HOH

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Components

#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.: 1 / 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 (E. coli) / Strain (production host): BL21(DE3)-V3R
References: UniProt: Q5VVY1, protein N-terminal monomethyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 26 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Aug 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→19.98 Å / Num. obs: 16827 / % possible obs: 94.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 25.74 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.06 / Rrim(I) all: 0.106 / Net I/σ(I): 10.2 / Num. measured all: 44067 / Scaling rejects: 0
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
2-2.052.60.7310311830.6230.5060.8711.791.7
8.95-45.62.50.0194531810.9990.0130.02343.179.6

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→18.98 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.893 / SU R Cruickshank DPI: 0.182 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.187 / SU Rfree Blow DPI: 0.168 / SU Rfree Cruickshank DPI: 0.166
Details: Intensities of only approx. 64 degrees of the data collection sweep were merged and used for model refinement. Subsequent diffraction images show ice rings, possibly due to malfunctioning ...Details: Intensities of only approx. 64 degrees of the data collection sweep were merged and used for model refinement. Subsequent diffraction images show ice rings, possibly due to malfunctioning crystal cooling. The protein was crystallized in the presence of a putative inhibitor, but electron density maps did not fully resolve the expected inhibitor.
RfactorNum. reflection% reflection
Rfree0.25 792 4.72 %
Rwork0.208 --
obs0.21 16794 93 %
Displacement parametersBiso max: 73.45 Å2 / Biso mean: 27.38 Å2 / Biso min: 11.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.1214 Å20 Å20 Å2
2--7.2593 Å20 Å2
3----7.1379 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2→18.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 53 63 1765
Biso mean--25.27 28.94 -
Num. residues----218
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d593SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes38HARMONIC2
X-RAY DIFFRACTIONt_gen_planes270HARMONIC5
X-RAY DIFFRACTIONt_it1728HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion223SEMIHARMONIC5
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_contact2036SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1728HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2345HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion15.49
LS refinement shellResolution: 2→2.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.259 128 4.32 %
Rwork0.225 2837 -
all-2965 -
obs--92.23 %

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