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- PDB-5cve: Crystal Structure of human NRMT1 in complex with dimethylated fly... -

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Basic information

Entry
Database: PDB / ID: 5cve
TitleCrystal Structure of human NRMT1 in complex with dimethylated fly H2B peptide and SAH
Components
  • N-terminal Xaa-Pro-Lys N-methyltransferase 1
  • N-terminal peptide from Histone H2B
KeywordsTRANSFERASE/PEPTIDE / N-terminal methyltransferase / TRANSFERASE-PEPTIDE 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 / E3 ubiquitin ligases ubiquitinate target proteins / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Ub-specific processing proteases ...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 / E3 ubiquitin ligases ubiquitinate target proteins / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Ub-specific processing proteases / protein methyltransferase activity / spindle organization / histone methyltransferase activity / chromosome segregation / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / protein-containing complex binding / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / Histone H2B signature. / Histone H2B / Histone H2B / Vaccinia Virus protein VP39 / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / Histone H2B signature. / Histone H2B / Histone H2B / Vaccinia Virus protein VP39 / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone H2B / N-terminal Xaa-Pro-Lys N-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsWu, R. / Li, H.
CitationJournal: Genes Dev. / Year: 2015
Title: Molecular basis for histone N-terminal methylation by NRMT1
Authors: Wu, R. / Yue, Y. / Zheng, X. / Li, H.
History
DepositionJul 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-terminal Xaa-Pro-Lys N-methyltransferase 1
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
D: N-terminal peptide from Histone H2B
E: N-terminal peptide from Histone H2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7226
Polymers56,9534
Non-polymers7692
Water13,583754
1
A: N-terminal Xaa-Pro-Lys N-methyltransferase 1
D: N-terminal peptide from Histone H2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8613
Polymers28,4762
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-5 kcal/mol
Surface area11370 Å2
MethodPISA
2
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
E: N-terminal peptide from Histone H2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8613
Polymers28,4762
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-6 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.836, 66.302, 68.730
Angle α, β, γ (deg.)90.000, 106.440, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-641-

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: 27589.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTMT1,NRMT1 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9BV86, protein N-terminal methyltransferase
#2: Protein/peptide N-terminal peptide from Histone H2B


Mass: 887.055 Da / Num. of mol.: 2 / Fragment: UNP residues 2-10 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P02283
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 754 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 0.2 M (NH4)Ac, 0.1 M Sodium citrate tribasic dihydrate, 24%(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2015 / Details: ADSC Quantum 315r
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 78798 / % possible obs: 99.2 % / Redundancy: 7.3 % / Biso Wilson estimate: 14.17 Å2 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.039 / Rrim(I) all: 0.105 / Χ2: 1.634 / Net I/av σ(I): 30.647 / Net I/σ(I): 7.8 / Num. measured all: 577246
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.537.30.81738960.8460.3230.8790.96598
1.53-1.557.40.73438680.880.2890.7890.98998.3
1.55-1.587.30.64738690.8950.2550.6961.00498.3
1.58-1.627.30.5539420.9190.2170.5921.03598.5
1.62-1.657.40.48838680.9430.1920.5251.06698.6
1.65-1.697.40.4439160.9460.1730.4731.07998.7
1.69-1.737.40.39338920.9550.1540.4231.10798.8
1.73-1.787.40.33439170.970.1320.3591.16898.9
1.78-1.837.40.27839150.9780.1090.2981.21799
1.83-1.897.40.23539500.9830.0930.2531.38799.2
1.89-1.967.40.19139220.9860.0750.2051.53599.3
1.96-2.047.40.15239220.990.060.1631.68599.4
2.04-2.137.40.13339920.990.0530.1431.89199.6
2.13-2.247.40.11339260.9940.0450.1221.9699.6
2.24-2.387.30.10839940.9940.0430.1162.09499.8
2.38-2.567.30.09639480.9950.0380.1032.14499.8
2.56-2.8270.08539750.9950.0350.0922.43999.9
2.82-3.237.10.06939900.9970.0280.0752.713100
3.23-4.077.30.05440170.9980.0210.0582.675100
4.07-507.30.0540790.9980.020.0542.49799.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
SCALAdata reduction
RefinementResolution: 1.5→32.118 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1795 2371 3.01 %Ramdom selection
Rwork0.1526 76416 --
obs0.1534 78787 99.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.39 Å2 / Biso mean: 17.9526 Å2 / Biso min: 6.87 Å2
Refinement stepCycle: final / Resolution: 1.5→32.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3741 0 52 754 4547
Biso mean--10.32 28.64 -
Num. residues----471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053906
X-RAY DIFFRACTIONf_angle_d1.055291
X-RAY DIFFRACTIONf_chiral_restr0.075581
X-RAY DIFFRACTIONf_plane_restr0.005682
X-RAY DIFFRACTIONf_dihedral_angle_d12.9521486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4982-1.52880.24531390.21054407X-RAY DIFFRACTION97
1.5288-1.5620.23011260.20214431X-RAY DIFFRACTION98
1.562-1.59830.25681300.18924441X-RAY DIFFRACTION98
1.5983-1.63830.20821520.17794424X-RAY DIFFRACTION99
1.6383-1.68260.25181410.17554468X-RAY DIFFRACTION99
1.6826-1.73210.1721380.16794483X-RAY DIFFRACTION99
1.7321-1.7880.19991500.16864440X-RAY DIFFRACTION99
1.788-1.85190.22361490.16834467X-RAY DIFFRACTION99
1.8519-1.92610.21031460.16434481X-RAY DIFFRACTION99
1.9261-2.01370.19161340.15414519X-RAY DIFFRACTION99
2.0137-2.11990.15111230.14534503X-RAY DIFFRACTION99
2.1199-2.25260.18361620.14394492X-RAY DIFFRACTION100
2.2526-2.42650.17181230.15424530X-RAY DIFFRACTION100
2.4265-2.67060.1881520.15744569X-RAY DIFFRACTION100
2.6706-3.05680.18611510.1534509X-RAY DIFFRACTION100
3.0568-3.85020.13831270.13474590X-RAY DIFFRACTION100
3.8502-32.12550.15361280.13534662X-RAY DIFFRACTION100

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