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- PDB-2rfj: Crystal structure of the bromo domain 1 in human bromodomain cont... -

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Basic information

Entry
Database: PDB / ID: 2rfj
TitleCrystal structure of the bromo domain 1 in human bromodomain containing protein, testis specific (BRDT)
ComponentsBromodomain testis-specific protein
KeywordsTRANSCRIPTION REGULATOR / BRDT / bromodomain containing protein testis specific / Structural Genomics Consortium / SGC / Nucleus / Transcription / Transcription regulation
Function / homology
Function and homology information


sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / localization / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding ...sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / localization / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding / transcription coactivator activity / chromatin remodeling / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / 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
Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsFilippakopoulos, P. / Salah, E. / Savitsky, P. / Keates, T. / Parizotto, E. / Elkins, J. / Pike, A.C.W. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. ...Filippakopoulos, P. / Salah, E. / Savitsky, P. / Keates, T. / Parizotto, E. / Elkins, J. / Pike, A.C.W. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Sundstrom, M. / 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
DepositionSep 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Bromodomain testis-specific protein
B: Bromodomain testis-specific protein
C: Bromodomain testis-specific protein


Theoretical massNumber of molelcules
Total (without water)42,4993
Polymers42,4993
Non-polymers00
Water4,558253
1
A: Bromodomain testis-specific protein


Theoretical massNumber of molelcules
Total (without water)14,1661
Polymers14,1661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain testis-specific protein


Theoretical massNumber of molelcules
Total (without water)14,1661
Polymers14,1661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Bromodomain testis-specific protein


Theoretical massNumber of molelcules
Total (without water)14,1661
Polymers14,1661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.935, 92.679, 100.107
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ARGARGGLNGLNAA27 - 1359 - 117
2THRTHRGLNGLNBB29 - 13511 - 117
3ASNASNMETMETCC30 - 13312 - 115

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Components

#1: Protein Bromodomain testis-specific protein / RING3-like protein


Mass: 14166.427 Da / Num. of mol.: 3 / Fragment: Bromo 1 domain: Residues 21-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRDT / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-R3 / References: UniProt: Q58F21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 47.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.20M Na/K tartrate, 20.0% PEG 3350, 10.0% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97866 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 22, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97866 Å / Relative weight: 1
ReflectionResolution: 2.05→50.063 Å / Num. all: 25870 / Num. obs: 24939 / % possible obs: 96.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 4.6
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 1 / Num. measured all: 8196 / Num. unique all: 2857 / Rsym value: 0.681 / % possible all: 77.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.34 Å
Translation2.47 Å46.34 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NXB

2nxb


Resolution: 2.05→50.063 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.16 / SU ML: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1249 5 %RANDOM
Rwork0.191 ---
all0.194 24883 --
obs0.194 24883 96.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.732 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2--0.54 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 0 253 2815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222622
X-RAY DIFFRACTIONr_bond_other_d0.0010.021762
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9663546
X-RAY DIFFRACTIONr_angle_other_deg0.99334317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25425.366123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65615461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.217156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022835
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02509
X-RAY DIFFRACTIONr_nbd_refined0.1930.2555
X-RAY DIFFRACTIONr_nbd_other0.1780.21662
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21251
X-RAY DIFFRACTIONr_nbtor_other0.0910.21232
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2190
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.25
X-RAY DIFFRACTIONr_mcbond_it4.14131651
X-RAY DIFFRACTIONr_mcbond_other1.9743613
X-RAY DIFFRACTIONr_mcangle_it4.77252543
X-RAY DIFFRACTIONr_scbond_it6.92281169
X-RAY DIFFRACTIONr_scangle_it8.048111003
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1358 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.390.5
BMEDIUM POSITIONAL0.390
CMEDIUM POSITIONAL0.440
AMEDIUM THERMAL1.512
BMEDIUM THERMAL1.70
CMEDIUM THERMAL1.560
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 71 -
Rwork0.222 1241 -
all-1312 -
obs--70.5 %
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)
11.41511.1255-1.02360.9127-1.14266.9128-0.1511-0.086-0.2206-0.1072-0.1124-0.18520.49570.14140.26340.16750.05220.0078-0.05430.0193-0.06340.89920.33327.713
22.2804-0.7018-0.20231.6524-2.37654.15850.0301-0.03940.0067-0.203-0.00370.15260.28070.2047-0.02640.1480.0291-0.0085-0.0218-0.0073-0.068946.79132.54212.865
30.92570.0986-0.81430.8186-0.24791.8272-0.0964-0.01460.02950.04990.01640.03310.12580.10750.080.1170.0383-0.0064-0.00190.0021-0.079239.83729.26326.92
41.35910.90112.09334.28753.32044.2362-0.20230.32610.1793-0.40920.164-0.0834-0.51620.27130.03830.2012-0.05510.0078-0.00010.0289-0.133257.23750.7788.163
51.07220.47320.94851.64751.4042.6476-0.15480.3206-0.0688-0.07480.1421-0.2022-0.24440.40720.01270.107-0.04060.02510.0762-0.0213-0.082562.49943.66711.603
60.69420.99350.47311.74660.66741.8462-0.06310.01090.0754-0.1011-0.03040.0791-0.16910.04460.09350.15560.0244-0.0267-0.0312-0.003-0.071950.15445.56413.589
71.0110.3440.50811.40510.07733.3048-0.1067-0.1340.01290.23320.1044-0.0261-0.27850.29420.00230.1275-0.0550.01320.0109-0.0313-0.106127.37851.95439.567
80.1333-0.08560.15763.45470.47551.6311-0.10750.00450.0092-0.08280.2058-0.0845-0.1040.4064-0.09830.0877-0.05310.00680.0497-0.0175-0.07432.17946.80432.078
91.2604-1.66520.70934.52881.41182.7682-0.043-0.1132-0.1417-0.10380.06370.2433-0.13260.0344-0.02060.1129-0.02990.0225-0.0168-0.0036-0.057219.90644.43732.931
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA27 - 519 - 33
2X-RAY DIFFRACTION2AA52 - 7334 - 55
3X-RAY DIFFRACTION3AA74 - 13556 - 117
4X-RAY DIFFRACTION4BB29 - 6511 - 47
5X-RAY DIFFRACTION5BB66 - 9248 - 74
6X-RAY DIFFRACTION6BB93 - 13575 - 117
7X-RAY DIFFRACTION7CC30 - 5612 - 38
8X-RAY DIFFRACTION8CC60 - 10142 - 83
9X-RAY DIFFRACTION9CC102 - 13384 - 115

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