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- PDB-2xb1: Crystal structure of the human Pygo2 PHD finger in complex with t... -

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Basic information

Entry
Database: PDB / ID: 2xb1
TitleCrystal structure of the human Pygo2 PHD finger in complex with the B9L HD1 domain
ComponentsPYGOPUS HOMOLOG 2, B-CELL CLL/LYMPHOMA 9-LIKE PROTEIN
KeywordsTRANSCRIPTION / FUSION PROTEIN / SIGNAL TRANSDUCTION / METAL BINDING / WNT PROTEINS
Function / homology
Function and homology information


histone acetyltransferase regulator activity / spermatid nucleus differentiation / regulation of mammary gland epithelial cell proliferation / beta-catenin-TCF complex / mammary gland development / regulation of cell morphogenesis / myoblast differentiation / lens development in camera-type eye / roof of mouth development / skeletal muscle cell differentiation ...histone acetyltransferase regulator activity / spermatid nucleus differentiation / regulation of mammary gland epithelial cell proliferation / beta-catenin-TCF complex / mammary gland development / regulation of cell morphogenesis / myoblast differentiation / lens development in camera-type eye / roof of mouth development / skeletal muscle cell differentiation / somatic stem cell population maintenance / developmental growth / canonical Wnt signaling pathway / positive regulation of epithelial to mesenchymal transition / kidney development / Deactivation of the beta-catenin transactivating complex / negative regulation of transforming growth factor beta receptor signaling pathway / Formation of the beta-catenin:TCF transactivating complex / brain development / fibrillar center / beta-catenin binding / histone binding / transcription by RNA polymerase II / transcription coactivator activity / chromatin binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
B Cell Lymphoma 9 / B-cell lymphoma 9, beta-catenin binding domain / B-cell lymphoma 9 protein / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger ...B Cell Lymphoma 9 / B-cell lymphoma 9, beta-catenin binding domain / B-cell lymphoma 9 protein / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / 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
DI(HYDROXYETHYL)ETHER / B-cell CLL/lymphoma 9-like protein / Pygopus homolog 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMiller, T.C. / Rutherford, T.J. / Johnson, C.M. / Fiedler, M. / Bienz, M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Allosteric Remodeling of the Histone H3 Binding Pocket in the Pygo2 Phd Finger Triggered by its Binding to the B9L/Bcl9 Co-Factor.
Authors: Miller, T.C. / Rutherford, T.J. / Johnson, C.M. / Fiedler, M. / Bienz, M.
History
DepositionApr 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2011Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYGOPUS HOMOLOG 2, B-CELL CLL/LYMPHOMA 9-LIKE PROTEIN
C: PYGOPUS HOMOLOG 2, B-CELL CLL/LYMPHOMA 9-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0879
Polymers22,5352
Non-polymers5527
Water3,405189
1
A: PYGOPUS HOMOLOG 2, B-CELL CLL/LYMPHOMA 9-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4904
Polymers11,2671
Non-polymers2233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: PYGOPUS HOMOLOG 2, B-CELL CLL/LYMPHOMA 9-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5975
Polymers11,2671
Non-polymers3294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.750, 69.730, 82.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PYGOPUS HOMOLOG 2, B-CELL CLL/LYMPHOMA 9-LIKE PROTEIN / PYGOPUS 2 / B-CELL LYMPHOMA 9-LIKE PROTEIN / BCL9-LIKE PROTEIN / BCL9-2 / B9L


Mass: 11267.499 Da / Num. of mol.: 2
Fragment: PHD FINGER AND HD1 DOMAIN, RESIDUES 325-387,232-266
Source method: isolated from a genetically manipulated source
Details: ARTIFICIAL LINKER BETWEEN PHD FINGER AND HD1 DOMAIN (7AA LINKER-GSGSGSG)
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM41-HPHD2GSGHD1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL / References: UniProt: Q9BRQ0, UniProt: Q86UU0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.3 Å3/Da / Density % sol: 46.12 % / Description: NONE
Crystal growDetails: 6% PEG 1000, 1.6 M (NH4)2SO4, 100 MM HEPES PH 7.5, 45 MM HCL

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.04
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2009 / Details: UNDULATOR
RadiationMonochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.9→38.75 Å / Num. obs: 18032 / % possible obs: 99.5 % / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.08 / Net I/σ(I): 6.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.358 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
iMOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VP7

2vp7


Resolution: 1.9→31.31 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.873 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES RESIDUAL ONLY ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21715 1287 7.1 %RANDOM
Rwork0.17122 ---
obs0.17441 16788 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.815 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 23 189 1678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211558
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.9372124
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6755207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16125.27872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0915246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.848156
X-RAY DIFFRACTIONr_chiral_restr0.1370.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021178
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_it0.8991.5982
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52721574
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6493576
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0984.5542
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 100 -
Rwork0.229 1209 -
obs--99.32 %
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)
13.61731.5849-0.99057.24172.88865.61450.0495-0.2214-0.28390.05170.086-0.56950.19510.4253-0.13550.11490.0365-0.03380.11550.00540.17495.9617-27.634935.2036
22.6684-0.06892.0132.5067-0.49846.02880.09970.1486-0.0564-0.1818-0.0093-0.14380.01440.2886-0.09040.11650.0162-0.00320.13680.00570.15462.2887-20.150433.6344
31.1917-0.00650.46134.4665-2.08053.87650.07510.068-0.1854-0.04830.0026-0.02710.14220.0451-0.07770.10430.0017-0.00390.1445-0.01520.1123-6.2076-17.161127.1354
42.87840.7955-0.52922.7894-1.5125.4787-0.0432-0.060.0826-0.1259-0.0087-0.0683-0.15360.26940.05190.10920.0072-0.01820.1396-0.00710.1587-3.9048-13.339936.6526
518.67055.9913-3.470527.72464.567814.9506-0.6565-1.95040.59520.52490.7206-0.23780.74261.8664-0.06420.0610.1294-0.0540.4103-0.03730.016-7.3242-17.000149.3407
64.2637-1.68620.69772.8901-0.03048.3394-0.1032-0.12580.18540.1043-0.008-0.266-0.61580.04370.11120.15730.0059-0.0120.12260.00580.1336-9.3819-10.656935.3379
75.4388-2.15631.73585.2627-8.932214.73780.14330.3082-0.11-0.41990.1470.35510.1895-0.1861-0.29020.14070.0258-0.02380.1440.00290.0992-14.5121-9.773626.625
811.5335-0.80755.11982.93582.651315.14990.2309-0.0901-0.22070.267-0.19510.4765-0.3154-0.6338-0.03580.23420.11330.00170.09770.03650.0693-15.5584-4.370823.0736
90.1933-2.8675-0.86727.37661.4816.6462-0.2172-0.08560.13690.42490.24020.1171-0.1038-0.1884-0.0230.19190.0506-0.03640.095-0.00640.1004-12.8145-2.660833.6211
103.2415-3.07631.21992.3301-0.97034.02940.0212-0.0304-0.4472-0.05290.06550.35940.1993-0.2889-0.08670.1019-0.0489-0.02740.10590.01490.1844-24.6235-27.35485.1477
112.33110.7627-0.33296.9255-3.25059.49170.0792-0.4719-0.05490.5951-0.02570.33860.0531-0.7354-0.05350.0651-0.02770.02340.21630.01760.1031-22.8796-22.170112.3703
121.60710.53591.23371.0325-0.13414.42290.05840.0785-0.00130.03970.0402-0.0069-0.1731-0.083-0.09860.10130.0037-0.00410.11970.00130.1439-19.3381-19.32244.0034
131.80210.7605-0.12624.7442.29132.51550.1064-0.1382-0.14950.1263-0.06810.05370.0815-0.004-0.03830.1183-0.0065-0.01460.15230.01910.0988-11.9549-17.087413.9747
142.51810.04390.15293.52182.33256.3056-0.0290.26670.0397-0.1544-0.02860.0867-0.2519-0.23290.05760.10880-0.02070.12940.01550.1549-13.1051-14.38050.6345
152.59810.8410.93723.08082.28934.77020.01610.07170.1392-0.3143-0.02330.1064-0.44510.08820.00720.1367-0.01070.00730.11660.01070.1282-7.6476-10.90396.1998
164.60624.5827-0.68686.7565.600421.02290.104-0.3195-0.08060.4558-0.0162-0.46110.3256-0.1699-0.08770.1158-0.0141-0.02760.1101-0.01680.1131-3.447-9.790216.6941
1718.8526-0.34753.75985.4639-5.784314.71830.036-0.09860.1270.3317-0.5174-0.5292-0.37990.72580.48140.1935-0.0673-0.02070.096-0.02840.0769-1.9208-4.077417.0547
181.96631.5175-1.18082.9288-1.58916.68170.00130.02390.1985-0.27110.0231-0.1680.0160.1594-0.02440.1688-0.0049-0.0010.0804-0.01350.129-4.6232-3.50617.2966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A326 - 337
2X-RAY DIFFRACTION2A338 - 356
3X-RAY DIFFRACTION3A357 - 369
4X-RAY DIFFRACTION4A370 - 383
5X-RAY DIFFRACTION5A384 - 389
6X-RAY DIFFRACTION6A235 - 244
7X-RAY DIFFRACTION7A245 - 250
8X-RAY DIFFRACTION8A251 - 256
9X-RAY DIFFRACTION9A257 - 266
10X-RAY DIFFRACTION10C325 - 335
11X-RAY DIFFRACTION11C336 - 345
12X-RAY DIFFRACTION12C346 - 356
13X-RAY DIFFRACTION13C357 - 369
14X-RAY DIFFRACTION14C370 - 389
15X-RAY DIFFRACTION15C235 - 245
16X-RAY DIFFRACTION16C246 - 251
17X-RAY DIFFRACTION17C252 - 257
18X-RAY DIFFRACTION18C258 - 266

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