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- PDB-3l42: PWWP domain of human bromodomain and PHD finger containing protein 1 -

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Basic information

Entry
Database: PDB / ID: 3l42
TitlePWWP domain of human bromodomain and PHD finger containing protein 1
ComponentsPeregrin
KeywordsTRANSCRIPTION / transcription regulation / histone h3 acetylation / chromatin modification / Structural Genomics / Structural Genomics Consortium / SGC / Activator / Bromodomain / Chromatin regulator / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Zinc-finger
Function / homology
Function and homology information


acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
BRPF1, PHD domain / Peregrin, 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. ...BRPF1, PHD domain / Peregrin, 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 C2H2 type domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / sad / Resolution: 1.3 Å
AuthorsTempel, W. / Zeng, H. / Ni, S. / Amaya, M.F. / Dong, A. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Tempel, W. / Zeng, H. / Ni, S. / Amaya, M.F. / Dong, A. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / 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
DepositionDec 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.type / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peregrin


Theoretical massNumber of molelcules
Total (without water)15,0764
Polymers15,0761
Non-polymers03
Water1,946108
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.352, 44.352, 122.722
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Peregrin / Bromodomain and PHD finger-containing protein 1 / BR140 protein


Mass: 15076.455 Da / Num. of mol.: 1 / Fragment: UNP residues 1079-1207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: P55201
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
1239.3THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion8.53.5M sodium formate, 0.1M TRIS-hydrochloride, pH 8.5, vapor diffusion, temperature 291K
2912vapor diffusion7.525% PEG3350, 0.1M ammonium sulfate, 0.1M HEPES, pH 7.5, vapor diffusion, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97711
ROTATING ANODERIGAKU FR-E21.5418
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.977111
21.54181
ReflectionResolution: 1.3→40 Å / Num. obs: 31403 / % possible obs: 99.9 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.056 / Χ2: 1.614 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.3213.80.46515441.4681,2100
1.32-1.3514.20.38715351.4651,2100
1.35-1.3714.30.34615221.4731,2100
1.37-1.414.30.29415441.3751,2100
1.4-1.4314.30.25315481.3531,2100
1.43-1.4614.40.21815211.3021,2100
1.46-1.514.30.16915441.2721,2100
1.5-1.5414.40.14315491.2851,2100
1.54-1.5914.40.12415441.2171,2100
1.59-1.6414.60.10315421.181,2100
1.64-1.714.50.09215621.21,2100
1.7-1.7614.60.07915481.1991,2100
1.76-1.8414.70.06815801.2521,2100
1.84-1.9414.90.05815451.3651,2100
1.94-2.06150.05715691.6511,2100
2.06-2.22150.05916002.2091,2100
2.22-2.45150.06115832.6331,2100
2.45-2.814.80.05216142.4241,2100
2.8-3.5314.30.04216492.331,299.9
3.53-4013.40.03917602.3841,298.5

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Phasing

PhasingMethod: sad

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.3→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.211 / SU B: 0.726 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY The structure was solved using the selenomethionene derivative crystallized in space group I222 and a copper ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY The structure was solved using the selenomethionene derivative crystallized in space group I222 and a copper rotating anode. The programs ARP/WARP, COOT and MOLPROBITY were also used during model refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1565 5.034 %RANDOM
Rwork0.209 ---
obs0.21 31089 99.926 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.096 Å2
Baniso -1Baniso -2Baniso -3
1--0.007 Å20 Å20 Å2
2---0.007 Å20 Å2
3---0.015 Å2
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 3 108 1094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221099
X-RAY DIFFRACTIONr_bond_other_d0.0010.02752
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.9771519
X-RAY DIFFRACTIONr_angle_other_deg0.96831864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3075153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24523.63644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5315189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.874156
X-RAY DIFFRACTIONr_chiral_restr0.1030.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211226
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02213
X-RAY DIFFRACTIONr_mcbond_it1.0961.5680
X-RAY DIFFRACTIONr_mcbond_other0.3081.5263
X-RAY DIFFRACTIONr_mcangle_it1.85521115
X-RAY DIFFRACTIONr_scbond_it2.4433419
X-RAY DIFFRACTIONr_scangle_it3.4554.5390
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 (%)
1.3-1.3340.2481190.25521312250100
1.334-1.370.2691070.23220712178100
1.37-1.410.2381010.23120242125100
1.41-1.4530.2181120.21419642076100
1.453-1.5010.2451170.20119182035100
1.501-1.5530.216870.17918501937100
1.553-1.6120.229780.19518231901100
1.612-1.6770.193930.1817161809100
1.677-1.7520.239870.19116641751100
1.752-1.8370.231850.19216161701100
1.837-1.9360.214860.19515061592100
1.936-2.0530.197820.19714351517100
2.053-2.1940.195690.19713741443100
2.194-2.3680.19720.20612701342100
2.368-2.5930.22540.19512041258100
2.593-2.8960.243620.21710651127100
2.896-3.3390.19520.2179741026100
3.339-4.0770.264550.20383789399.888
4.077-5.7130.287230.2168070499.858
5.713-300.429240.34440244795.302

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