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- PDB-3tlp: Crystal structure of the fourth bromodomain of human poly-bromodo... -

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Basic information

Entry
Database: PDB / ID: 3tlp
TitleCrystal structure of the fourth bromodomain of human poly-bromodomain containing protein 1 (PB1)
ComponentsProtein polybromo-1
KeywordsTRANSCRIPTION / PB1 / polybromo 1 isoform 1 / BAF180 / Polybromo-1D / PBRM1 / BRG1-associated factor 180 / Structural Genomics Consortium / SGC / Bromodomain
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
NICKEL (II) ION / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.13 Å
AuthorsFilippakopoulos, P. / Felletar, I. / Picaud, S. / Keates, T. / Muniz, J. / Krojer, T. / Allerston, C.K. / Latwiel, S. / von Delft, F. / Arrowsmith, C.H. ...Filippakopoulos, P. / Felletar, I. / Picaud, S. / Keates, T. / Muniz, J. / Krojer, T. / Allerston, C.K. / Latwiel, S. / 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
DepositionAug 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,1636
Polymers34,9282
Non-polymers2354
Water1,40578
1
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6404
Polymers17,4641
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5232
Polymers17,4641
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.431, 60.220, 109.907
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 / BRG1-associated factor 180 / BAF180 / Polybromo-1D


Mass: 17464.084 Da / Num. of mol.: 2 / Fragment: UNP residues 496-637
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAF180, PB1, PBRM1 / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q86U86
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / 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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG_MME_2000, 0.015M NiCl, 0.1M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 4.4 % / Av σ(I) over netI: 9.9 / Number: 82363 / Rsym value: 0.062 / D res high: 2.13 Å / D res low: 19.747 Å / Num. obs: 18871 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
6.7419.7594.310.0220.0223.9
4.766.7498.510.030.034.1
3.894.7699.310.0310.0314.4
3.373.899910.0410.0414.2
3.013.3799.410.070.074.5
2.753.0199.810.1250.1254.5
2.552.7599.810.2210.2214.2
2.382.5599.710.3680.3684.5
2.252.3899.810.5690.5694.5
2.132.2599.810.880.884.3
ReflectionResolution: 2.13→19.75 Å / Num. all: 18984 / Num. obs: 18871 / % possible obs: 99.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.13-2.254.30.880.91170927380.8899.8
2.25-2.384.50.5691.31158825520.56999.8
2.38-2.554.50.36821099424200.36899.7
2.55-2.754.20.2213.3973122970.22199.8
2.75-3.014.50.1255.9943920760.12599.8
3.01-3.374.50.0710.2849718930.0799.4
3.37-3.894.20.04116.8708916900.04199
3.89-4.764.40.03120.7624914320.03199.3
4.76-6.744.10.0321.5462111390.0398.5
6.74-19.753.90.02223.524466340.02294.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 52.22 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.75 Å
Translation2.5 Å19.75 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
GDAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3HMF, 2OO1, 3DAI, 3HMH, 2OSS, 2OUO, 3D7C, 3DWY

3hmf

2oo1

3dai

3hmh

2oss

2ouo

3d7c

3dwy


Resolution: 2.13→19.75 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2298 / WRfactor Rwork: 0.188 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8454 / SU B: 9.063 / SU ML: 0.124 / SU R Cruickshank DPI: 0.1948 / SU Rfree: 0.1796 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 973 5.2 %RANDOM
Rwork0.2014 ---
all0.2037 19003 --
obs0.2037 18831 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 194.25 Å2 / Biso mean: 50.8461 Å2 / Biso min: 21.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.13→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 4 78 1971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221922
X-RAY DIFFRACTIONr_bond_other_d0.0050.021380
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9852577
X-RAY DIFFRACTIONr_angle_other_deg1.17333353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3155234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49323.76393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79215370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7081517
X-RAY DIFFRACTIONr_chiral_restr0.080.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212116
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02381
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 72 -
Rwork0.344 1154 -
all-1226 -
obs--99.92 %
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)
10.1385-0.1967-0.01341.38320.410.45540.0811-0.07740.0784-0.2609-0.0019-0.1848-0.0152-0.0452-0.07920.1105-0.00550.05660.0738-0.01750.11993.43730.809823.4788
20.6657-0.22210.54810.4664-0.2610.4866-0.0927-0.0975-0.02390.02980.07590.0232-0.092-0.07610.01680.04080.0199-0.0010.12080.01030.1164-14.2743-11.37177.65
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A478 - 596
2X-RAY DIFFRACTION2B481 - 597

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