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- PDB-3pfs: PWWP Domain of Human Bromodomain and PHD finger-containing protein 3 -

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Basic information

Entry
Database: PDB / ID: 3pfs
TitlePWWP Domain of Human Bromodomain and PHD finger-containing protein 3
ComponentsBromodomain and PHD finger-containing protein 3
KeywordsPROTEIN BINDING / Structural Genomics / Structural Genomics Consortium / SGC / PWWP Domain
Function / homology
Function and homology information


MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / positive regulation of DNA replication / Platelet degranulation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription ...MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / positive regulation of DNA replication / Platelet degranulation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / extracellular region / zinc ion binding / nucleus / cytosol
Similarity search - Function
BRPF3, ePHD domain / SH3 type barrels. - #140 / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif ...BRPF3, ePHD domain / SH3 type barrels. - #140 / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / 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 / SH3 type barrels. / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
Bromodomain and PHD finger-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsLam, R. / Zeng, H. / Kania, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2011
Title: Structural and histone binding ability characterizations of human PWWP domains.
Authors: Wu, H. / Zeng, H. / Lam, R. / Tempel, W. / Amaya, M.F. / Xu, C. / Dombrovski, L. / Qiu, W. / Wang, Y. / Min, J.
History
DepositionOct 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_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: Bromodomain and PHD finger-containing protein 3
B: Bromodomain and PHD finger-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6015
Polymers36,3742
Non-polymers2273
Water2,450136
1
A: Bromodomain and PHD finger-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3483
Polymers18,1871
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain and PHD finger-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2522
Polymers18,1871
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.412, 134.522, 30.226
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-120-

HOH

21A-121-

HOH

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Components

#1: Protein Bromodomain and PHD finger-containing protein 3


Mass: 18187.018 Da / Num. of mol.: 2 / Fragment: PWWP domain (UNP Residues 1056-1195)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF3, KIAA1286 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2 / References: UniProt: Q9ULD4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 1.91 Å3/Da / Density % sol: 35.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG4000, 0.2M Ammonium Sulfate, 0.1M Sodium Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010
Details: Rosenbaum-Rock high-resolution double-crystal monochromator
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.9→33.631 Å / Num. obs: 22879 / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.091 / Χ2: 1.005 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.9760.47622090.9861100
1.97-2.056.10.34622380.9911100
2.05-2.146.10.26922721.0381100
2.14-2.256.10.20522241.0141100
2.25-2.396.10.15322631.0071100
2.39-2.586.10.1322760.9761100
2.58-2.8460.09622801.0121100
2.84-3.2560.0723080.9821100
3.25-4.095.90.06223271.004199.9
4.09-33.6315.60.04824821.042199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.02 Å34.21 Å
Translation2.02 Å34.21 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.6.0081refinement
PDB_EXTRACT3.1data extraction
EPICS-basedbeamline controldata collection
dataacquisition systemsdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X4W

2x4w


Resolution: 1.9→33.631 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.261 / WRfactor Rwork: 0.213 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.492 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 1170 5.1 %RANDOM
Rwork0.2109 ---
obs0.2134 22830 99.86 %-
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 max: 64.71 Å2 / Biso mean: 22.3843 Å2 / Biso min: 8.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2093 0 7 136 2236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222149
X-RAY DIFFRACTIONr_angle_refined_deg1.1992.0112920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2595262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.66823.56387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71215381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8491516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221600
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9490.275810.241523161899.135
1.949-2.0030.287860.2021559164699.939
2.003-2.0610.277690.20314801549100
2.061-2.1240.27790.2031453153399.935
2.124-2.1940.248750.19414151490100
2.194-2.2710.261750.2081358143599.861
2.271-2.3560.313790.21813231402100
2.356-2.4520.263750.21912491324100
2.452-2.5610.277600.23912341294100
2.561-2.6860.303580.23911841242100
2.686-2.8310.308570.25611071164100
2.831-3.0020.329650.23410831148100
3.002-3.2090.27530.239771030100
3.209-3.4660.264570.209945100499.801
3.466-3.7960.257620.195868930100
3.796-4.2420.162390.18378182199.878
4.242-4.8950.215250.167721746100
4.895-5.9870.215360.19961264999.846
5.987-8.4340.22160.214501517100
8.434-67.2610.211230.21228732196.573
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)
11.1719-0.35740.39780.82760.24640.789-0.0025-0.03580.04650.0009-0.01920.06880.0724-0.05980.02170.0311-0.0103-0.00110.0126-0.01390.031320.958-9.85-5.764
21.27110.1259-0.19580.879-0.12570.6905-0.0255-0.0918-0.0796-0.07910.04360.0372-0.0411-0.0257-0.0180.0545-0.00210.01410.01460.00610.016227.002-39.936-2.354
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1061 - 1194
2X-RAY DIFFRACTION2B1062 - 1191

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