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- PDB-5c6s: Human Bromodomain and PHD Finger Containing 1, PWWP domain in com... -

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Basic information

Entry
Database: PDB / ID: 5c6s
TitleHuman Bromodomain and PHD Finger Containing 1, PWWP domain in complex with XST005904a
ComponentsPeregrin
KeywordsTRANSCRIPTION / PEREGRIN / PROTEIN BR140 / HISTONE H3 ACETYLATION / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / 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 / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / 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 / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
BRPF1, PHD domain / Peregrin, ePHD domain / : / SH3 type barrels. - #140 / 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 / : / SH3 type barrels. - #140 / 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 C2H2 type domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
isoquinoline-3-carboxylic acid / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 Å
AuthorsDONG, A. / DOBROVETSKY, E. / MADER, P. / Santhakumar, S. / TEMPEL, W. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Human Bromodomain and PHD Finger Containing 1, PWWP domain in complex with XST005904a
Authors: DOBROVETSKY, E. / DONG, A. / MADER, P. / Santhakumar, S. / TEMPEL, W. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / Structural Genomics Consortium (SGC)
History
DepositionJun 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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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)15,52319
Polymers15,0761
Non-polymers44718
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.453, 44.453, 125.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1316-

UNX

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 15076.455 Da / Num. of mol.: 1 / Fragment: PWWP domain (UNP residues 1079-1207)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-PRARE2 / References: UniProt: P55201

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Non-polymers , 5 types, 192 molecules

#2: Chemical ChemComp-4K8 / isoquinoline-3-carboxylic acid


Mass: 173.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7NO2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 15 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG 3350, 0.2M LiSO4, 0.1M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 32041 / % possible obs: 99.6 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.032 / Rrim(I) all: 0.111 / Χ2: 2.218 / Net I/av σ(I): 41.573 / Net I/σ(I): 8.1 / Num. measured all: 400377
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.3-1.3210.40.97615540.7850.3040.95999.5
1.32-1.3511.40.80315800.9080.2421.0281000.839
1.35-1.3712.10.82915500.9050.2441.0311000.865
1.37-1.412.80.71315800.9340.2051.1321000.742
1.4-1.4313.20.61915850.9540.1761.231000.644
1.43-1.4613.50.61315560.9610.1731.2331000.637
1.46-1.513.40.49515950.970.141.4561000.515
1.5-1.5413.50.42815700.9780.1211.6151000.445
1.54-1.5913.40.36415980.980.1031.7611000.379
1.59-1.6413.30.32815680.9760.0941.9741000.341
1.64-1.713.10.27515930.9830.0792.1741000.287
1.7-1.7612.90.23815870.9870.0692.36299.90.248
1.76-1.8412.50.20316000.9910.062.69899.60.212
1.84-1.9411.90.17115900.9920.0513.10999.50.179
1.94-2.0611.60.14915990.9910.0453.55999.70.156
2.06-2.2212.10.12616310.9940.0373.57999.90.131
2.22-2.4512.60.11216210.9950.0333.45499.90.117
2.45-2.812.80.09816470.9940.0283.2299.60.102
2.8-3.5312.30.08616650.9960.0253.274990.089
3.53-5011.20.07917720.9960.0243.40296.60.083

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0123refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 1.3→41.92 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.537 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 963 3 %RANDOM
Rwork0.1937 ---
obs0.1944 30947 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.25 Å2 / Biso mean: 22.002 Å2 / Biso min: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20 Å2
2---1.27 Å20 Å2
3---2.55 Å2
Refinement stepCycle: final / Resolution: 1.3→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1006 0 34 180 1220
Biso mean--38.8 33.29 -
Num. residues----126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191225
X-RAY DIFFRACTIONr_bond_other_d0.0020.021158
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9731695
X-RAY DIFFRACTIONr_angle_other_deg0.92432677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5275163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25823.63655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47115212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.967159
X-RAY DIFFRACTIONr_chiral_restr0.090.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211503
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02284
X-RAY DIFFRACTIONr_mcbond_it1.0662.029584
X-RAY DIFFRACTIONr_mcbond_other1.0662.032585
X-RAY DIFFRACTIONr_mcangle_it1.6923.052750
LS refinement shellResolution: 1.297→1.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 72 -
Rwork0.326 2012 -
all-2084 -
obs--89.44 %

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