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- PDB-3o70: PHD-type zinc finger of human PHD finger protein 13 -

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Basic information

Entry
Database: PDB / ID: 3o70
TitlePHD-type zinc finger of human PHD finger protein 13
ComponentsPHD finger protein 13
KeywordsPROTEIN BINDING / PHF13 / Structural Genomics Consortium / SGC / structural genomics / PHD-type zinc finger / zinc ion binding
Function / homology
Function and homology information


chromatin-protein adaptor activity / mitotic chromosome condensation / regulation of DNA repair / methylated histone binding / chromosome segregation / mitotic cell cycle / cell division / chromatin binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
PHF13, PHD finger / PhD finger domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHD finger protein 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsLam, R. / Bian, C.B. / Xu, C. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Elife / Year: 2016
Title: PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3.
Authors: Chung, H.R. / Xu, C. / Fuchs, A. / Mund, A. / Lange, M. / Staege, H. / Schubert, T. / Bian, C. / Dunkel, I. / Eberharter, A. / Regnard, C. / Klinker, H. / Meierhofer, D. / Cozzuto, L. / ...Authors: Chung, H.R. / Xu, C. / Fuchs, A. / Mund, A. / Lange, M. / Staege, H. / Schubert, T. / Bian, C. / Dunkel, I. / Eberharter, A. / Regnard, C. / Klinker, H. / Meierhofer, D. / Cozzuto, L. / Winterpacht, A. / Di Croce, L. / Min, J. / Will, H. / Kinkley, S.
History
DepositionJul 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: PHD finger protein 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3145
Polymers7,9991
Non-polymers3154
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PHD finger protein 13
hetero molecules

A: PHD finger protein 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,62910
Polymers15,9992
Non-polymers6308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area1960 Å2
ΔGint-13 kcal/mol
Surface area8040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.315, 58.315, 73.231
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PHD finger protein 13


Mass: 7999.359 Da / Num. of mol.: 1 / Fragment: PHD-type zinc finger (unp residues 232-281)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF13 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2 / References: UniProt: Q86YI8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 20% PEG8000, 0.1M CHES pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 24, 2010 / Details: double crystal monochromator
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 11409 / % possible obs: 99.9 % / Redundancy: 15.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.85-1.89140.496199.9
1.89-1.9415.60.3981100
1.94-1.9915.80.3141100
1.99-2.05160.231100
2.05-2.1215.90.1811100
2.12-2.19160.1361100
2.19-2.28160.1111100
2.28-2.3915.90.0951100
2.39-2.5115.90.0741100
2.51-2.6715.90.0651100
2.67-2.8715.80.0621100
2.87-3.1615.70.0671100
3.16-3.6215.50.061100
3.62-4.5615.20.0361100
4.56-5013.60.035199.1

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.85 Å / D res low: 29.16 Å / FOM acentric: 0.458 / FOM centric: 0.178 / Reflection acentric: 9304 / Reflection centric: 2013
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1001.8529.1693042013
ANO_10.57601.8529.1693040
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_17.97-29.16007995
ISO_15.75-7.970016698
ISO_14.72-5.7500228100
ISO_14.1-4.720027498
ISO_13.68-4.10031999
ISO_13.36-3.6800355100
ISO_13.12-3.3600385103
ISO_12.92-3.120042297
ISO_12.75-2.9200452103
ISO_12.61-2.7500485102
ISO_12.49-2.6100506106
ISO_12.39-2.4900539104
ISO_12.29-2.390055189
ISO_12.21-2.2900588106
ISO_12.13-2.2100598105
ISO_12.07-2.130063099
ISO_12.01-2.070064398
ISO_11.95-2.0100670103
ISO_11.9-1.9500697103
ISO_11.85-1.900717105
ANO_17.97-29.160.3650790
ANO_15.75-7.970.21401660
ANO_14.72-5.750.25602280
ANO_14.1-4.720.28602740
ANO_13.68-4.10.34103190
ANO_13.36-3.680.503550
ANO_13.12-3.360.46403850
ANO_12.92-3.120.47704220
ANO_12.75-2.920.46704520
ANO_12.61-2.750.4804850
ANO_12.49-2.610.49405060
ANO_12.39-2.490.58205390
ANO_12.29-2.390.73105510
ANO_12.21-2.290.7705880
ANO_12.13-2.210.82305980
ANO_12.07-2.130.89406300
ANO_12.01-2.070.92806430
ANO_11.95-2.010.96106700
ANO_11.9-1.950.97306970
ANO_11.85-1.90.98607170
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
140.82354.6379.021ZN37.22.44
241.45661.059-2.566ZN39.592.34
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
7.97-29.160.7250.2247995
5.75-7.970.7450.18316698
4.72-5.750.6550.22228100
4.1-4.720.6590.17627498
3.68-4.10.610.15131999
3.36-3.680.5520.153355100
3.12-3.360.5670.152385103
2.92-3.120.5720.18342297
2.75-2.920.5940.194452103
2.61-2.750.5980.22485102
2.49-2.610.6010.187506106
2.39-2.490.5640.188539104
2.29-2.390.4710.16855189
2.21-2.290.4490.187588106
2.13-2.210.410.165598105
2.07-2.130.3540.17563099
2.01-2.070.3180.14764398
1.95-2.010.2790.155670103
1.9-1.950.2540.167697103
1.85-1.90.2360.163717105
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 11317
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.48-10058.60.798501
4.28-5.4856.40.91513
3.71-4.2855.10.91508
3.35-3.71550.92509
3.1-3.3556.60.913514
2.91-3.149.50.904504
2.76-2.91540.908501
2.64-2.7653.40.892502
2.53-2.6454.50.886508
2.44-2.5348.60.871508
2.36-2.4455.50.833508
2.29-2.3661.20.833501
2.23-2.2959.20.849501
2.17-2.23570.853508
2.12-2.1760.80.866512
2.07-2.1261.40.855508
2.03-2.0767.60.854517
1.99-2.0365.50.851516
1.95-1.9966.40.831516
1.92-1.9566.70.817540
1.88-1.92730.78550
1.85-1.8876.40.708572

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM6.1phasing
REFMACrefmac_5.6.0081refinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→27.38 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.913 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18763 540 4.8 %RANDOM
Rwork0.18405 ---
obs0.18422 10775 99.96 %-
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: 43.436 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms443 0 14 41 498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022464
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.965620
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.435554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14822.63219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1891584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.227153
X-RAY DIFFRACTIONr_chiral_restr0.0850.267
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021337
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 33 -
Rwork0.213 788 -
obs--99.88 %
Refinement TLS params.Method: refined / Origin x: 3.696 Å / Origin y: 19.711 Å / Origin z: 34.077 Å
111213212223313233
T0.0948 Å2-0.0131 Å20.0296 Å2-0.0337 Å2-0.0199 Å2--0.0577 Å2
L1.864 °2-0.4929 °2-0.5548 °2-1.1896 °20.3576 °2--3.1831 °2
S0.0415 Å °0.0492 Å °-0.0618 Å °-0.1132 Å °-0.1485 Å °0.1372 Å °0.1948 Å °-0.1676 Å °0.107 Å °

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