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- PDB-6kdr: Crystal structure of human NRMT2 in complex with human centromere... -

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Basic information

Entry
Database: PDB / ID: 6kdr
TitleCrystal structure of human NRMT2 in complex with human centromere protein B peptide
Components
  • Alpha N-terminal protein methyltransferase 1B
  • Peptide from Major centromere autoantigen B
KeywordsTRANSFERASE / core methyltransferase fold
Function / homology
Function and homology information


protein N-terminal monomethyltransferase / N-terminal protein amino acid methylation / N-terminal protein N-methyltransferase activity / satellite DNA binding / centromeric DNA binding / condensed chromosome, centromeric region / chromosome, centromeric region / pericentric heterochromatin / chromosome / sequence-specific DNA binding ...protein N-terminal monomethyltransferase / N-terminal protein amino acid methylation / N-terminal protein N-methyltransferase activity / satellite DNA binding / centromeric DNA binding / condensed chromosome, centromeric region / chromosome, centromeric region / pericentric heterochromatin / chromosome / sequence-specific DNA binding / nuclear body / chromatin binding / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Centromere protein CENP-B, C-terminal domain / CENP-B, dimerisation domain superfamily / Centromere protein B dimerisation domain / CENP-B N-terminal DNA-binding domain / DNA binding HTH domain, Psq-type / Psq-type HTH domain profile. / DDE superfamily endonuclease domain / HTH CenpB-type DNA-binding domain / DDE superfamily endonuclease / Tc5 transposase DNA-binding domain ...Centromere protein CENP-B, C-terminal domain / CENP-B, dimerisation domain superfamily / Centromere protein B dimerisation domain / CENP-B N-terminal DNA-binding domain / DNA binding HTH domain, Psq-type / Psq-type HTH domain profile. / DDE superfamily endonuclease domain / HTH CenpB-type DNA-binding domain / DDE superfamily endonuclease / Tc5 transposase DNA-binding domain / CENPB-type HTH domain profile. / Putative DNA-binding domain in centromere protein B, mouse jerky and transposases. / Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / Vaccinia Virus protein VP39 / Homeobox-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Major centromere autoantigen B / N-terminal Xaa-Pro-Lys N-methyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.112 Å
AuthorsYue, Y. / Li, H.
CitationJournal: to be published
Title: Substrate-enzyme engagement regulates state-specific alpha-N methylation of NRMT2
Authors: Wu, R. / Yue, Y. / Zheng, X. / Li, H.
History
DepositionJul 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: database_2 / struct_ref
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref.entity_id
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
A: Alpha N-terminal protein methyltransferase 1B
B: Alpha N-terminal protein methyltransferase 1B
D: Peptide from Major centromere autoantigen B
E: Peptide from Major centromere autoantigen B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,40112
Polymers57,2504
Non-polymers1,1518
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-50 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.548, 96.534, 100.213
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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

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


Mass: 27519.480 Da / Num. of mol.: 2 / Fragment: Protein N-terminal methyltransferase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: METTL11B, C1orf184, NRMT2 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5VVY1, protein N-terminal monomethyltransferase
#2: Protein/peptide Peptide from Major centromere autoantigen B / / Centromere protein B / CENP-B


Mass: 1105.313 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P07199

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Non-polymers , 4 types, 254 molecules

#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 / Feature type: SUBJECT OF INVESTIGATION / References: UniProt: P07199*PLUS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.98 Å3/Da / Density % sol: 58.73 % / Mosaicity: 0.574 ° / Mosaicity esd: 0.007 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.3 / Details: 0.1M Tris pH 8.3, 6% w/v Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2019 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 39673 / % possible obs: 99.8 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.043 / Rrim(I) all: 0.127 / Χ2: 1.585 / Net I/σ(I): 9.7 / Num. measured all: 344656
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.148.71.36119530.8290.4781.4450.50299.3
2.14-2.188.51.1619550.8760.4141.2330.51499.5
2.18-2.228.60.96919430.8740.3441.030.53999.6
2.22-2.268.90.93719770.8230.3310.9960.87899.8
2.26-2.3190.76319290.9030.2660.8090.743100
2.31-2.3790.60219550.9530.2080.6380.6499.9
2.37-2.428.90.51619810.9550.180.5470.67399.8
2.42-2.498.70.46219570.960.1640.4910.76899.9
2.49-2.568.60.37219520.9620.1330.3960.89199.9
2.56-2.659.30.30319720.9810.1040.3210.91399.8
2.65-2.749.20.23919410.9850.0820.2531.174100
2.74-2.859.20.19919870.9880.0690.2111.27599.9
2.85-2.988.90.15919860.9880.0560.1691.52299.9
2.98-3.148.70.12919720.9930.0460.1371.84100
3.14-3.3390.10520020.9950.0370.1112.535100
3.33-3.598.60.0919960.9950.0320.0953.0299.9
3.59-3.9580.07520000.9950.0280.083.42699.8
3.95-4.528.50.06220170.9970.0220.0663.56499.9
4.52-5.78.10.05620340.9970.0210.063.28399.7
5.7-507.60.05421640.9980.0210.0583.36699.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
PHENIX1.14rc3_3206refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CVD

5cvd


Resolution: 2.112→44.473 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.95
RfactorNum. reflection% reflection
Rfree0.2047 1937 4.89 %
Rwork0.1783 --
obs0.1894 39605 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.99 Å2 / Biso mean: 43.636 Å2 / Biso min: 19.13 Å2
Refinement stepCycle: final / Resolution: 2.112→44.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 73 246 3937
Biso mean--35.86 44.45 -
Num. residues----455
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1122-2.1650.30031090.2399239390
2.165-2.22360.25151310.24032675100
2.2236-2.2890.32591330.23112685100
2.289-2.36290.28091470.222671100
2.3629-2.44730.27631570.22312667100
2.4473-2.54530.27551230.2262684100
2.5453-2.66110.30591480.2182678100
2.6611-2.80140.26871360.21512681100
2.8014-2.97690.25341480.21172700100
2.9769-3.20670.22861270.20582735100
3.2067-3.52930.19161280.18762733100
3.5293-4.03970.18791630.17322709100
4.0397-5.08840.16311390.14922774100
5.0884-44.4730.19181480.16742883100

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