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- PDB-4lc2: Crystal structure of the bromodomain of human BRPF1B -

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Basic information

Entry
Database: PDB / ID: 4lc2
TitleCrystal structure of the bromodomain of human BRPF1B
ComponentsPeregrin
KeywordsDNA BINDING PROTEIN / Bromodomain and PHD finger-containing protein 1 / Protein Br140 / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
BRPF1, PHD domain / Peregrin, ePHD domain / : / : / 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. ...BRPF1, PHD domain / Peregrin, ePHD domain / : / : / 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 C2H2 type domain profile. / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type profile. / Zinc finger C2H2-type / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsTallant, C. / Nunez-Alonso, G. / Savitsky, P. / Picaud, S. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of the bromodomain of human BRPF1B
Authors: Tallant, C. / Nunez-Alonso, G. / Savitsky, P. / Picaud, S. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, H.C. / Edwards, M.A. / Bountra, C. / Knapp, S.
History
DepositionJun 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Sep 20, 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

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Assembly

Deposited unit
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8283
Polymers13,7041
Non-polymers1242
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.835, 60.835, 63.679
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-914-

HOH

21A-951-

HOH

31A-1004-

HOH

41A-1016-

HOH

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Components

#1: Protein Peregrin / Bromodomain and PHD finger-containing protein 1 / Protein Br140


Mass: 13703.698 Da / Num. of mol.: 1 / Fragment: unp residues 626-740
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BR140, BRPF1, BRPF1B / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: P55201
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 20% PEG3350 0.1 M bis tris propane, 10% ethylene glycol 0.15 M sodium nitrate, pH 7.8, 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: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→19 Å / Num. all: 16843 / Num. obs: 16793 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.026 / Rsym value: 0.026 / Net I/σ(I): 40.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.65-1.745.50.1355.823790.13598.3
1.74-1.846.80.0987.922970.098100
1.84-1.976.90.06911.121510.069100
1.97-2.136.90.04616.220030.046100
2.13-2.3370.03619.418880.036100
2.33-2.6170.02922.116690.029100
2.61-3.0170.02524.315210.025100
3.01-3.6970.0222812770.022100
3.69-5.226.90.01832.610220.018100
5.22-196.40.01921.75860.01997.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.63 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å17.56 Å
Translation3.5 Å17.56 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of PDB ENTRIES 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, 3DWY

1dvv

1x0j

3dai

3hmh

2grc

2oo1

2oss

2ouo

3d7c

3dwy


Resolution: 1.65→19 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2241 / WRfactor Rwork: 0.1754 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8648 / SU B: 3.331 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0901 / SU Rfree: 0.0967 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 847 5.1 %RANDOM
Rwork0.1744 ---
all0.1767 16838 --
obs0.1767 16767 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.16 Å2 / Biso mean: 25.5295 Å2 / Biso min: 8.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.19 Å2-0 Å2
2---0.19 Å2-0 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 8 121 1065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.019991
X-RAY DIFFRACTIONr_bond_other_d0.0010.02945
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.9811340
X-RAY DIFFRACTIONr_angle_other_deg0.88332173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7555123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04224.07454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12515183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.127159
X-RAY DIFFRACTIONr_chiral_restr0.0950.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211136
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02239
X-RAY DIFFRACTIONr_mcbond_it4.9222.878465
X-RAY DIFFRACTIONr_mcbond_other4.6512.832464
X-RAY DIFFRACTIONr_mcangle_it5.6625.285582
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 59 -
Rwork0.188 1131 -
all-1190 -
obs--96.2 %
Refinement TLS params.Method: refined / Origin x: 12.7879 Å / Origin y: 25.2852 Å / Origin z: 11.1287 Å
111213212223313233
T0.0158 Å20.0028 Å20.0184 Å2-0.0863 Å2-0.0143 Å2--0.0522 Å2
L1.1357 °20.8595 °20.3537 °2-1.2574 °20.5639 °2--0.3429 °2
S-0.0258 Å °-0.1778 Å °-0.031 Å °-0.0178 Å °-0.0269 Å °-0.0312 Å °0.0213 Å °-0.0194 Å °0.0528 Å °

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