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- PDB-3lyi: PWWP Domain of Human Bromodomain-Containing Protein 1 -

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Basic information

Entry
Database: PDB / ID: 3lyi
TitlePWWP Domain of Human Bromodomain-Containing Protein 1
ComponentsBromodomain-containing protein 1
KeywordsTRANSCRIPTION / histone H3 acetylation / Structural Genomics Consortium / SGC / Bromodomain / Chromatin regulator
Function / homology
Function and homology information


unmodified histone reader activity / histone H3-K14 acetyltransferase complex / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / erythrocyte maturation / histone reader activity / response to immobilization stress / response to electrical stimulus / Regulation of TP53 Activity through Acetylation ...unmodified histone reader activity / histone H3-K14 acetyltransferase complex / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / erythrocyte maturation / histone reader activity / response to immobilization stress / response to electrical stimulus / Regulation of TP53 Activity through Acetylation / positive regulation of erythrocyte differentiation / HATs acetylate histones / perikaryon / nuclear speck / chromatin remodeling / dendrite / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
BRPF2, ePHD domain / BRPF2, PHD 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. ...BRPF2, ePHD domain / BRPF2, PHD 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
CYSTEINESULFONIC ACID / Bromodomain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLam, R. / Zeng, H. / Ni, S. / 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
DepositionFeb 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 1
B: Bromodomain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7873
Polymers28,6182
Non-polymers1691
Water1,40578
1
A: Bromodomain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4782
Polymers14,3091
Non-polymers1691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)14,3091
Polymers14,3091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.029, 46.085, 130.712
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain-containing protein 1 / BR140-like protein


Mass: 14308.836 Da / Num. of mol.: 2 / Fragment: PWWP Domain, residues 925-1049
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD1, BRL, BRPF2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-V2R-pRARE2 / References: UniProt: O95696
#2: Chemical ChemComp-OCS / CYSTEINESULFONIC ACID


Type: L-peptide linking / Mass: 169.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG2000-MME, 0.15M KBr, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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
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: 2.1→50 Å / Num. obs: 16475 / % possible obs: 99 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.074 / Χ2: 1.007 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1850.49515540.949195.3
2.18-2.265.60.44515701.129197.1
2.26-2.376.30.41916201.005199.8
2.37-2.496.80.30916260.948199.3
2.49-2.656.90.21716410.94199.6
2.65-2.8570.14916420.977199.5
2.85-3.1470.09616421.113199.6
3.14-3.597.30.07116810.956199.7
3.59-4.527.70.06816931.0521100
4.52-507.40.03618061.004199.4

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.36 Å37.67 Å
Translation2.36 Å37.67 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.005data extraction
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L42

3l42


Resolution: 2.1→37.66 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 1 / SU B: 13.125 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED. unknown ligand was not modeled.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 827 5 %RANDOM
Rwork0.234 ---
obs0.236 16421 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 124.8 Å2 / Biso mean: 59.069 Å2 / Biso min: 24.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 10 78 1880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221847
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.9812494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7435222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10623.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87915343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0231512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221344
X-RAY DIFFRACTIONr_mcbond_it0.6861.51130
X-RAY DIFFRACTIONr_mcangle_it1.24821834
X-RAY DIFFRACTIONr_scbond_it1.823717
X-RAY DIFFRACTIONr_scangle_it2.8934.5660
LS refinement shellResolution: 2.1→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 54 -
Rwork0.264 1052 -
all-1106 -
obs--92.09 %
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)
11.3321-0.199-0.25832.766-0.25780.9082-0.0143-0.0805-0.01290.11650.02440.1593-0.0071-0.0455-0.010.12080.00790.02630.12-0.02020.105111.2237.145-27.618
26.8521-3.5722-0.22855.5212.46572.51310.0672-0.22970.40190.1896-0.5810.26050.3083-0.32690.51380.3566-0.1260.14980.4328-0.31930.21980.12525.247-6.232
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A928 - 1047
2X-RAY DIFFRACTION2B931 - 1048

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