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- PDB-5r4v: XChem fragment screen -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF ... -

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Basic information

Entry
Database: PDB / ID: 5r4v
TitleXChem fragment screen -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF THE HUMAN ATAD2 in complex with N13475a
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


nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome ...nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / 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) / Bromodomain-like / Histone Acetyltransferase; Chain A / ATPase, AAA-type, core / 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) / Bromodomain-like / Histone Acetyltransferase; Chain A / ATPase, AAA-type, core / 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
Chem-JMM / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.29 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)16,3878
Polymers15,5131
Non-polymers8757
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.190, 80.190, 140.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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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, adenosinetriphosphatase
#2: Chemical ChemComp-JMM / [4-(cyclopropanecarbonyl)piperazin-1-yl](furan-2-yl)methanone


Mass: 248.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 1.29→69.45 Å / Num. obs: 67524 / % possible obs: 100 % / Redundancy: 15.9 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.015 / Rrim(I) all: 0.061 / Net I/σ(I): 25.1 / Num. measured all: 1070783 / 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
1.29-1.327.91.4283869448840.5330.5351.5281.4100
5.77-69.4516.20.0311483291510.0080.03288.299.8

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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: 1.29→69.45 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.985 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1526 3409 5.1 %RANDOM
Rwork0.1327 ---
obs0.1337 64030 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 529.72 Å2 / Biso mean: 19.496 Å2 / Biso min: 9.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.05 Å2-0 Å2
2---0.11 Å20 Å2
3---0.36 Å2
Refinement stepCycle: final / Resolution: 1.29→69.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 58 237 1379
Biso mean--36.76 36.13 -
Num. residues----130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0141241
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171167
X-RAY DIFFRACTIONr_angle_refined_deg1.9021.7071693
X-RAY DIFFRACTIONr_angle_other_deg1.5471.6272716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6465153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.35920.83384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39115228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0371516
X-RAY DIFFRACTIONr_chiral_restr0.1010.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021458
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02274
X-RAY DIFFRACTIONr_mcbond_it1.5521.552549
X-RAY DIFFRACTIONr_mcbond_other1.5511.557550
X-RAY DIFFRACTIONr_mcangle_it2.1012.331693
X-RAY DIFFRACTIONr_rigid_bond_restr2.79332403
LS refinement shellResolution: 1.29→1.323 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 259 -
Rwork0.276 4615 -
all-4874 -
obs--99.88 %

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