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- PDB-3ep0: Methyltransferase domain of human PR domain-containing protein 12 -

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Basic information

Entry
Database: PDB / ID: 3ep0
TitleMethyltransferase domain of human PR domain-containing protein 12
ComponentsPR domain zinc finger protein 12
KeywordsTRANSFERASE / PR domain-containing protein 12 / PR domain zinc finger protein 12 / Structural Genomics / Structural Genomics Consortium / SGC / DNA-binding / Metal-binding / Nucleus / Transcription / Transcription regulation / Zinc / Zinc-finger
Function / homology
Function and homology information


: / : / histone methyltransferase binding / detection of temperature stimulus involved in sensory perception of pain / sensory perception of pain / neurogenesis / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / neuron projection development / methylation ...: / : / histone methyltransferase binding / detection of temperature stimulus involved in sensory perception of pain / sensory perception of pain / neurogenesis / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / neuron projection development / methylation / regulation of gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
PR-domain zinc finger protein PRDM12 / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain profile. / SET domain / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...PR-domain zinc finger protein PRDM12 / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain profile. / SET domain / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Beta Complex / Mainly Beta
Similarity search - Domain/homology
PR domain zinc finger protein 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAmaya, M.F. / Zeng, H. / Loppnau, P. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Min, J. / Plotnikov, A.N. ...Amaya, M.F. / Zeng, H. / Loppnau, P. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Min, J. / Plotnikov, A.N. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of methyltransferase domain of human PR Domain-containing protein 12.
Authors: Zeng, H. / Amaya, M.F. / Loppnau, P. / Min, J. / Plotnikov, A.N. / Wu, H.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PR domain zinc finger protein 12
B: PR domain zinc finger protein 12


Theoretical massNumber of molelcules
Total (without water)38,1872
Polymers38,1872
Non-polymers00
Water1,22568
1
A: PR domain zinc finger protein 12


Theoretical massNumber of molelcules
Total (without water)19,0931
Polymers19,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PR domain zinc finger protein 12


Theoretical massNumber of molelcules
Total (without water)19,0931
Polymers19,0931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.882, 34.358, 103.739
Angle α, β, γ (deg.)90.000, 131.090, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PR domain zinc finger protein 12 / PR domain-containing protein 12


Mass: 19093.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDM12, PFM9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H4Q4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Purified PRDM12 was crystallized using hanging drop vapor diffusion method at 293K by mixing the protein solution with the reservoir solution containing 19% PEG 2,000 MME, 0.1 M KSCN., VAPOR ...Details: Purified PRDM12 was crystallized using hanging drop vapor diffusion method at 293K by mixing the protein solution with the reservoir solution containing 19% PEG 2,000 MME, 0.1 M KSCN., VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54178 Å
DetectorDate: Sep 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 21829

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DAL

3dal


Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.893 / Highest resolution: 2.1 Å / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.916 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1124 5.1 %RANDOM
Rwork0.257 ---
obs0.259 21829 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 46.15 Å2 / Biso mean: 24.308 Å2 / Biso min: 9.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å21.15 Å2
2---0.14 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 0 68 1809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221781
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9522419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7845220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86125.21171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02415286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.198154
X-RAY DIFFRACTIONr_chiral_restr0.0750.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021326
X-RAY DIFFRACTIONr_nbd_refined0.2020.2721
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21202
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2100
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.26
X-RAY DIFFRACTIONr_mcbond_it0.8481.51148
X-RAY DIFFRACTIONr_mcangle_it1.38821792
X-RAY DIFFRACTIONr_scbond_it1.6963759
X-RAY DIFFRACTIONr_scangle_it2.5264.5627
LS refinement shellResolution: 2.099→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 67 -
Rwork0.305 1363 -
all-1430 -
obs--88.76 %

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