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- PDB-5r4w: XChem fragment screen -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF ... -

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Basic information

Entry
Database: PDB / ID: 5r4w
TitleXChem fragment screen -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF THE HUMAN ATAD2 in complex with N13501a
ComponentsATPase family AAA domain-containing protein 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PanDDA / SGC - Diamond I04-1 fragment screening / XChemExplorer / ATPASE FAMILY / AAA DOMAIN CONTAINING 2 / ANCCA / AAA+ NUCLEAR COREGULATOR CANCER-ASSOCIATED PRO2000 PROTEIN / TWO AAA DOMAIN CONTAINING PROTEIN / SGC / STRUCTURAL GENOMICS CONSORTIUM / ATP-BINDING / BROMODOMAIN / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / SIGNALING PROTEIN / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / nucleus
Similarity search - Function
ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain ...ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
methyl 4-[(trifluoroacetyl)amino]benzoate / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.47 Å
AuthorsTalon, R. / Krojer, T. / Fairhead, M. / Sethi, R. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Wright, N. ...Talon, R. / Krojer, T. / Fairhead, M. / Sethi, R. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Wright, N. / MacLean, E. / Zhang, R. / Dias, A. / Brennan, P.E. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
CitationJournal: To Be Published
Title: XChem fragment screen
Authors: Talon, R. / Krojer, T. / Fairhead, M. / Sethi, R. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Wright, N. / MacLean, E. / Zhang, R. / Dias, A. / Brennan, ...Authors: Talon, R. / Krojer, T. / Fairhead, M. / Sethi, R. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Wright, N. / MacLean, E. / Zhang, R. / Dias, A. / Brennan, P.E. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
History
DepositionFeb 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATPase family AAA domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2008
Polymers15,5131
Non-polymers6887
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.470, 80.470, 139.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1321-

HOH

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Components

#1: Protein ATPase family AAA domain-containing protein 2 / AAA nuclear coregulator cancer-associated protein / ANCCA


Mass: 15512.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PL18, EC: 3.6.1.3
#2: Chemical ChemComp-RWP / methyl 4-[(trifluoroacetyl)amino]benzoate


Mass: 247.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8F3NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.2 Å3/Da / Density % sol: 70.7 % / Mosaicity: 0 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2.2M ammonium sulfate, 0.1M bis-tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.47→69.65 Å / Num. obs: 46087 / % possible obs: 100 % / Redundancy: 18.2 % / CC1/2: 1 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.022 / Rrim(I) all: 0.095 / Net I/σ(I): 20.9 / Num. measured all: 840275 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.47-1.5114.71.8854862533130.5540.5081.9541.5100
6.57-69.6515.80.0241025864810.0060.02591.299.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
Aimless0.5.17data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3DAI

3dai


Resolution: 1.47→62.4 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.848 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1612 2344 5.1 %RANDOM
Rwork0.1277 ---
obs0.1293 43667 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 497.83 Å2 / Biso mean: 25.049 Å2 / Biso min: 11.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.11 Å2-0 Å2
2---0.23 Å20 Å2
3---0.74 Å2
Refinement stepCycle: final / Resolution: 1.47→62.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 43 223 1350
Biso mean--60.2 39.95 -
Num. residues----130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131223
X-RAY DIFFRACTIONr_bond_other_d0.0050.0171145
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.6851665
X-RAY DIFFRACTIONr_angle_other_deg1.5291.5952660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7095153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30920.94185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62815229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.581516
X-RAY DIFFRACTIONr_chiral_restr0.10.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021427
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02273
X-RAY DIFFRACTIONr_mcbond_it2.9012.098550
X-RAY DIFFRACTIONr_mcbond_other2.9022.104551
X-RAY DIFFRACTIONr_mcangle_it3.773.138693
X-RAY DIFFRACTIONr_rigid_bond_restr3.47332363
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 177 -
Rwork0.251 3128 -
all-3305 -
obs--99.91 %

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