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- PDB-3ljw: Crystal Structure of the Second Bromodomain of Human Polybromo -

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Basic information

Entry
Database: PDB / ID: 3ljw
TitleCrystal Structure of the Second Bromodomain of Human Polybromo
ComponentsProtein polybromo-1
KeywordsTRANSCRIPTION / ALPHA Helix / Alternative splicing / Bromodomain / Chromatin regulator / DNA-binding / Nucleus / Phosphoprotein / Transcription regulation
Function / homology
Function and homology information


regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle ...regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription elongation by RNA polymerase II / positive regulation of cell differentiation / kinetochore / RMTs methylate histone arginines / nuclear matrix / mitotic cell cycle / chromatin remodeling / negative regulation of cell population proliferation / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Protein polybromo-1, Bromodomain 5 / Remodelling complex subunit Rsc/polybromo / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group ...Protein polybromo-1, Bromodomain 5 / Remodelling complex subunit Rsc/polybromo / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsCharlop-Powers, Z. / Zhou, M.M. / Zeng, L. / Zhang, Q.
CitationJournal: Cell Res. / Year: 2010
Title: Structural insights into selective histone H3 recognition by the human Polybromo bromodomain 2.
Authors: Charlop-Powers, Z. / Zeng, L. / Zhang, Q. / Zhou, M.M.
History
DepositionJan 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 15, 2020Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs ..._reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs
Revision 1.3Sep 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 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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.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_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

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Assembly

Deposited unit
A: Protein polybromo-1
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3205
Polymers27,1792
Non-polymers1413
Water12,394688
1
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6492
Polymers13,5901
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6723
Polymers13,5901
Non-polymers822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.964, 78.964, 50.651
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Protein polybromo-1 / hPB1 / Polybromo-1D / BRG1-associated factor 180 / BAF180


Mass: 13589.646 Da / Num. of mol.: 2 / Fragment: Bromodomain 2 (UNP residues 174-293)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PB1, PBRM1 / Plasmid: pGEX 4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86U86
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 3.35 Å3/Da / Density % sol: 63.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 35% PEG 4000, 10 mM Sodium Acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97854 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 12, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 1.455→50 Å / Num. obs: 59763 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 3.7 % / Biso Wilson estimate: 12.38 Å2 / Rsym value: 0.069 / Net I/σ(I): 35.4
Reflection shellResolution: 1.51→1.57 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 6.17 / Num. unique obs: 6101 / Rsym value: 0.215 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G0J

3g0j


Resolution: 1.501→28.34 Å / SU ML: 0.14 / σ(F): 0.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 1920 3.61 %Random
Rwork0.1727 ---
obs0.1735 53142 94.17 %-
all-55433 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.314 Å2 / ksol: 0.376 e/Å3
Refinement stepCycle: LAST / Resolution: 1.501→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 9 688 2562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061907
X-RAY DIFFRACTIONf_angle_d0.9272575
X-RAY DIFFRACTIONf_dihedral_angle_d13.029707
X-RAY DIFFRACTIONf_chiral_restr0.058291
X-RAY DIFFRACTIONf_plane_restr0.005329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5014-1.55510.21851870.19664975X-RAY DIFFRACTION92
1.5551-1.61730.2091910.18545141X-RAY DIFFRACTION94
1.6173-1.69090.20511970.18595128X-RAY DIFFRACTION94
1.6909-1.780.2231870.17865151X-RAY DIFFRACTION95
1.78-1.89150.21651900.17855075X-RAY DIFFRACTION93
1.8915-2.03760.19971910.18165203X-RAY DIFFRACTION96
2.0376-2.24250.22282020.16975233X-RAY DIFFRACTION96
2.2425-2.56680.18261950.16955165X-RAY DIFFRACTION95
2.5668-3.23320.17751960.16835192X-RAY DIFFRACTION95
3.2332-28.34460.17571840.15714959X-RAY DIFFRACTION91

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