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- PDB-2zfu: Structure of the methyltransferase-like domain of nucleomethylin -

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Basic information

Entry
Database: PDB / ID: 2zfu
TitleStructure of the methyltransferase-like domain of nucleomethylin
ComponentsCerebral protein 1
KeywordsNUCLEAR PROTEIN / NUCLEOLAR PROTEIN / SAM-BINDING PROTEIN / protein structure / Nucleus / Phosphoprotein
Function / homology
Function and homology information


regulation of transcription by glucose / regulation of cell cycle => GO:0051726 / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / S-adenosylmethionine-dependent methyltransferase activity / intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to glucose starvation / methylated histone binding / Transferases; Transferring one-carbon groups; Methyltransferases ...regulation of transcription by glucose / regulation of cell cycle => GO:0051726 / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / S-adenosylmethionine-dependent methyltransferase activity / intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to glucose starvation / methylated histone binding / Transferases; Transferring one-carbon groups; Methyltransferases / SIRT1 negatively regulates rRNA expression / rRNA processing / methylation / nucleolus / RNA binding / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Ribosomal RNA-processing protein 8, N-terminal domain / Ribosomal RNA processing protein 8 / Ribosomal RNA-processing protein 8, N-terminal domain / Hypothetical methyltransferase / UbiE/COQ5 methyltransferase, conserved site / Vaccinia Virus protein VP39 / Arc Repressor Mutant, subunit A / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle ...Ribosomal RNA-processing protein 8, N-terminal domain / Ribosomal RNA processing protein 8 / Ribosomal RNA-processing protein 8, N-terminal domain / Hypothetical methyltransferase / UbiE/COQ5 methyltransferase, conserved site / Vaccinia Virus protein VP39 / Arc Repressor Mutant, subunit A / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Ribosomal RNA-processing protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsMinami, H. / Hashimoto, H. / Murayama, A. / Yanagisawa, J. / Sato, M. / Shimizu, T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Epigenetic control of rDNA loci in response to intracellular energy status
Authors: Murayama, A. / Ohmori, K. / Fujimura, A. / Minami, H. / Yasuzawa-Tanaka, K. / Kuroda, T. / Oie, S. / Daitoku, H. / Okuwaki, M. / Nagata, K. / Fukamizu, A. / Kimura, K. / Shimizu, T. / Yanagisawa, J.
History
DepositionJan 14, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cerebral protein 1
B: Cerebral protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3634
Polymers48,5942
Non-polymers7692
Water5,098283
1
A: Cerebral protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6812
Polymers24,2971
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cerebral protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6812
Polymers24,2971
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.810, 43.810, 403.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Cerebral protein 1 / Nucleomethylin


Mass: 24297.004 Da / Num. of mol.: 2
Fragment: methyltransferase-like domain, UNP residues 242-456
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0409 / Plasmid: pGEX4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43159
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG 8000, 200mM Ammonium Sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONPhoton Factory BL-5A20.97912,0.97931,0.96408
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 9, 2006
ADSC QUANTUM 3152CCDMar 5, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979121
30.979311
40.964081
ReflectionResolution: 2→67.27 Å / Num. all: 28996 / Num. obs: 28996 / % possible obs: 98 % / Redundancy: 11 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.284 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→36.52 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 9.725 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23066 1467 5.1 %RANDOM
Rwork0.19161 ---
obs0.19361 27381 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.008 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20.18 Å20 Å2
2--0.36 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2→36.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 52 283 3634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223427
X-RAY DIFFRACTIONr_bond_other_d0.0010.022383
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9934648
X-RAY DIFFRACTIONr_angle_other_deg0.8635768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9035421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90822.949156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97715555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.51532
X-RAY DIFFRACTIONr_chiral_restr0.0740.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023805
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02727
X-RAY DIFFRACTIONr_nbd_refined0.2070.2779
X-RAY DIFFRACTIONr_nbd_other0.1890.22662
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21692
X-RAY DIFFRACTIONr_nbtor_other0.0850.21812
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2267
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1770.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.213
X-RAY DIFFRACTIONr_mcbond_it0.7251.52722
X-RAY DIFFRACTIONr_mcbond_other0.1141.5846
X-RAY DIFFRACTIONr_mcangle_it0.80223410
X-RAY DIFFRACTIONr_scbond_it1.44631499
X-RAY DIFFRACTIONr_scangle_it2.0974.51238
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 98 -
Rwork0.224 1830 -
obs--90.43 %
Refinement TLS params.Method: refined / Origin x: 16.5328 Å / Origin y: 9.045 Å / Origin z: -17.3057 Å
111213212223313233
T-0.0961 Å2-0.002 Å20.0044 Å2--0.0819 Å20.0296 Å2---0.038 Å2
L0.4226 °2-0.3035 °20.349 °2-0.9044 °2-0.6864 °2--1.8237 °2
S0.0006 Å °-0.0264 Å °0.0314 Å °-0.0673 Å °-0.0042 Å °-0.0548 Å °0.0785 Å °-0.1079 Å °0.0036 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A243 - 454
2X-RAY DIFFRACTION1B243 - 454

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