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- PDB-3mb4: Crystal Structure of the fifth Bromodomain of Human Poly-bromodom... -

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Basic information

Entry
Database: PDB / ID: 3mb4
TitleCrystal Structure of the fifth Bromodomain of Human Poly-bromodomain containing protein 1 (PB1) with NMP
ComponentsProtein polybromo-1
KeywordsTRANSCRIPTION / PB1 / polybromo 1 isoform 1 / BAF180 / Polybromo-1D / PBRM1 / BRG1-associated factor 180 / Structural Genomics Consortium / SGC / Bromodomain / Chromatin regulator / DNA-binding / Nucleus / Phosphoprotein / Transcription regulation
Function / homology
Function and homology information


regulation of G0 to G1 transition / RSC-type complex / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / nuclear chromosome / positive regulation of double-strand break repair / 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 / RSC-type complex / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / nuclear chromosome / positive regulation of double-strand break repair / 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 / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / kinetochore / RMTs methylate histone arginines / nuclear matrix / mitotic cell cycle / chromatin remodeling / negative regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Protein polybromo-1, Bromodomain 5 / Remodelling complex subunit Rsc/polybromo / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / 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 domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
1-methylpyrrolidin-2-one / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Keates, T. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Histone recognition and large-scale structural analysis of the human bromodomain family.
Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S.
History
DepositionMar 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,94613
Polymers29,2962
Non-polymers65011
Water3,747208
1
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9075
Polymers14,6481
Non-polymers2594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0408
Polymers14,6481
Non-polymers3927
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.957, 52.221, 134.964
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 Protein polybromo-1 / hPB1 / Polybromo-1D / BRG1-associated factor 180 / BAF180


Mass: 14648.000 Da / Num. of mol.: 2 / Fragment: UNP residues 645-766
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAF180, PB1, PBRM1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q86U86
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MB3 / 1-methylpyrrolidin-2-one


Mass: 99.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.15M NaNO3 25% PEG 3350 10% Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. all: 36073 / Num. obs: 36037 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.067 / Rsym value: 0.064 / Net I/σ(I): 25
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.955 / Mean I/σ(I) obs: 1.97 / Num. unique all: 3536 / Rsym value: 0.817 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.4 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.25 Å
Translation2.5 Å19.25 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3G0J

3g0j


Resolution: 1.66→19.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.853 / SU B: 4.137 / SU ML: 0.072 / SU R Cruickshank DPI: 0.097 / SU Rfree: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1795 5 %RANDOM
Rwork0.197 ---
all0.198 35920 --
obs0.198 35898 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 103.33 Å2 / Biso mean: 37.169 Å2 / Biso min: 19.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å20 Å2
2---0.68 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.66→19.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 38 208 2142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221991
X-RAY DIFFRACTIONr_bond_other_d0.0010.021424
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9972668
X-RAY DIFFRACTIONr_angle_other_deg0.9343.0013457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9915231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20924.21195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33515394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5281514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212126
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02380
X-RAY DIFFRACTIONr_mcbond_it2.631170
X-RAY DIFFRACTIONr_mcbond_other0.8863455
X-RAY DIFFRACTIONr_mcangle_it3.65551905
X-RAY DIFFRACTIONr_scbond_it6.5618821
X-RAY DIFFRACTIONr_scangle_it7.75711762
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 129 -
Rwork0.457 2455 -
all-2584 -
obs--99.31 %
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)
11.216-0.2821-0.100417.3075-7.19754.38820.24270.2891-0.1237-0.727-0.2061-0.25170.1980.0992-0.03650.08170.0472-0.00930.104-0.02640.039940.802746.351312.5815
25.4574-1.7434-3.7185.2902-0.85799.24640.0681-0.1525-0.02510.9820.11830.6512-0.3287-0.6204-0.18640.2181-0.00580.13770.08860.00160.088626.508645.193328.8582
30.33340.17441.419934.2938-21.710321.67070.0417-0.0914-0.06070.03250.73210.88530.0842-1.414-0.77390.0220.0388-0.00760.3415-0.01130.050630.391253.228316.7917
42.3881-1.02270.6584.9753-4.17735.6310.0454-0.120.22950.8775-0.0388-0.1129-0.6130.0658-0.00660.2298-0.0324-0.01390.0131-0.00930.027836.502752.540425.0042
56.71654.9618-4.743616.4234-10.546314.0686-0.0458-0.0447-0.00380.9542-0.3084-0.7367-0.33240.79690.35430.1451-0.0174-0.11640.06380.02260.095944.224243.732825.3955
60.16051.03041.68168.830511.142118.269-0.0070.02920.0131-0.71420.11240.1664-0.3581-0.0008-0.10530.1377-0.0049-0.05970.15820.12880.148623.738624.01376.2037
719.6491-12.37254.249217.4733-2.31356.14190.13990.0030.2730.12940.08870.6283-0.5512-0.3559-0.22860.09760.02660.03710.03660.03850.125423.424337.758120.5457
87.1631-1.87764.72564.7554-2.88486.8915-0.2407-0.15230.22510.63260.0685-0.59740.25940.12730.17220.22010.0524-0.1180.0257-0.02160.086138.069124.137328.0594
92.4899-1.048-0.54155.84562.95668.7388-0.03890.0623-0.0760.24560.06190.06590.4086-0.11-0.0230.0257-0.0079-0.0060.02290.02010.027228.593919.270718.0548
107.70935.08756.23488.30627.991724.4290.03890.00520.16760.5507-0.29360.62350.9032-1.30910.25460.1066-0.03980.09830.1020.01770.130318.68626.246222.9174
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A620 - 648
2X-RAY DIFFRACTION2A649 - 674
3X-RAY DIFFRACTION3A675 - 682
4X-RAY DIFFRACTION4A683 - 707
5X-RAY DIFFRACTION5A708 - 734
6X-RAY DIFFRACTION6B619 - 641
7X-RAY DIFFRACTION7B642 - 651
8X-RAY DIFFRACTION8B652 - 671
9X-RAY DIFFRACTION9B672 - 707
10X-RAY DIFFRACTION10B708 - 734

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