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- PDB-3ihx: Methyltransferase domain of human PR domain-containing protein 10 -

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Basic information

Entry
Database: PDB / ID: 3ihx
TitleMethyltransferase domain of human PR domain-containing protein 10
ComponentsPR domain zinc finger protein 10
KeywordsTRANSFERASE / PRDM10 / Methyltransferase / Structural Genomics / Structural Genomics Consortium / SGC / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


chromatin => GO:0000785 / transcription repressor complex / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / regulation of gene expression / positive regulation of transcription by RNA polymerase II / DNA binding / metal ion binding / nucleus
Similarity search - Function
Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Beta-clip-like / SET domain / Zinc finger, C2H2 type / SET domain profile. / SET domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...Zinc-finger double-stranded RNA-binding / Zinc finger, double-stranded RNA binding / Beta-clip-like / SET domain / Zinc finger, C2H2 type / SET domain profile. / SET domain / 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 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAmaya, M.F. / Dombrovski, L. / Ni, S. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Min, J. / Plotnikov, A.N. ...Amaya, M.F. / Dombrovski, L. / Ni, S. / 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: Methyltransferase domain of human PR domain-containing protein 10
Authors: Amaya, M.F. / Dombrovski, L. / Ni, S. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Botchkarev, A. / Min, J. / Plotnikov, A.N. / Wu, H. / Structural Genomics Consortium (SGC)
History
DepositionJul 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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 10
B: PR domain zinc finger protein 10
C: PR domain zinc finger protein 10
D: PR domain zinc finger protein 10


Theoretical massNumber of molelcules
Total (without water)71,5984
Polymers71,5984
Non-polymers00
Water93752
1
A: PR domain zinc finger protein 10


Theoretical massNumber of molelcules
Total (without water)17,9001
Polymers17,9001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PR domain zinc finger protein 10


Theoretical massNumber of molelcules
Total (without water)17,9001
Polymers17,9001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PR domain zinc finger protein 10


Theoretical massNumber of molelcules
Total (without water)17,9001
Polymers17,9001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PR domain zinc finger protein 10


Theoretical massNumber of molelcules
Total (without water)17,9001
Polymers17,9001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.864, 94.864, 76.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
PR domain zinc finger protein 10 / PR domain-containing protein 10 / Tristanin


Mass: 17899.568 Da / Num. of mol.: 4 / Fragment: UNP Residues 188 to 339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDM10, KIAA1231, PFM7, TRIS / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NQV6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG3350, 0.2NH4oAC, Bis -6.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorDate: Jul 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 25428

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DB5, 3EP0

3db5

3ep0


Resolution: 2.5→94.86 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 31.521 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2978 976 4.2 %RANDOM
Rwork0.24179 ---
obs0.24407 22254 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.711 Å2
Baniso -1Baniso -2Baniso -3
1--2.54 Å20 Å20 Å2
2---2.54 Å20 Å2
3---5.07 Å2
Refinement stepCycle: LAST / Resolution: 2.5→94.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 0 52 3834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223893
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.9455325
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7345484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5322.988164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33115517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8921519
X-RAY DIFFRACTIONr_chiral_restr0.1030.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213026
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6121.52472
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12123905
X-RAY DIFFRACTIONr_scbond_it1.99931421
X-RAY DIFFRACTIONr_scangle_it3.1374.51420
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 56 -
Rwork0.373 1478 -
obs--87.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.0764-0.4136-1.9824.1975-1.29880.8901-0.0475-0.6892-0.12340.06180.20430.0340.02290.1484-0.15680.3069-0.0295-0.01670.4255-0.24380.441510.3114-64.8778-1.3956
27.8988-1.02650.00254.19330.30423.0343-0.1511-0.4809-0.47260.17870.47120.3816-0.0033-0.0378-0.32010.1565-0.02540.06140.3436-0.01870.3361-0.618-64.5819-0.1087
33.44271.18671.29015.94070.36431.9154-0.47580.5362-0.1544-0.27360.5679-0.68670.04350.1758-0.09210.1642-0.11620.01460.2658-0.06650.200221.9182-37.23244.2196
45.7508-0.0338-1.24064.0455-0.92972.1291-0.198-0.6559-0.42380.2340.23130.3218-0.3075-0.0598-0.03330.16370.01470.07330.19980.09960.2978-22.1347-57.82860.6057
514.34310.44087.18122.54341.20833.9854-1.0586-0.08141.0432-0.29650.25260.839-0.64350.04830.8060.4482-0.0645-0.22880.21060.16110.459-9.79-31.577-4.7128
613.04632.00133.70955.09680.5263.0561-0.9130.10411.0503-0.15380.46660.4454-0.33730.25450.44630.2755-0.0845-0.15850.24590.10280.14681.5703-31.7897-0.1638
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 91
2X-RAY DIFFRACTION2A92 - 146
3X-RAY DIFFRACTION3B5 - 148
4X-RAY DIFFRACTION4C11 - 148
5X-RAY DIFFRACTION5D7 - 93
6X-RAY DIFFRACTION6D94 - 147

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