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- PDB-4qsw: Structure of the bromodomain of human ATPase family AAA domain-co... -

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Basic information

Entry
Database: PDB / ID: 4qsw
TitleStructure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) in complex with 5-methyl uridine
ComponentsATPase family AAA domain-containing protein 2
KeywordsSIGNALING PROTEIN / Structural Genomics Consortium (SGC) / bromodomain / actyl-lysine binding / ATPase family AAA domain-containing protein 2 / epigenetics
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
5-methyluridine / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChaikuad, A. / Felletar, I. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: MedChemComm / Year: 2014
Title: Structure-based approaches towards identification of fragments for the low-druggability ATAD2 bromodomain
Authors: Chaikuad, A. / Petros, A.M. / Fedorov, O. / Xu, J. / Knapp, S.
History
DepositionJul 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
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: ATPase family AAA domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1188
Polymers15,4541
Non-polymers6657
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.590, 79.590, 138.421
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1383-

HOH

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Components

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


Mass: 15453.514 Da / Num. of mol.: 1 / Fragment: bromodomain (residues 981-1108)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-R3-pRARE2 / References: UniProt: Q6PL18, EC: 3.6.1.3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-38T / 5-methyluridine / 5-Methyluridine


Mass: 258.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 4.09 Å3/Da / Density % sol: 69.96 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: apo crystals grew in 1.8-2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 5.5-6.5. Soaking performed in 28-32% PEG 3350, 50 mM bis-tris pH 5.5, 50 mM ammonium phosphate and 20% ethylene glycol, ...Details: apo crystals grew in 1.8-2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 5.5-6.5. Soaking performed in 28-32% PEG 3350, 50 mM bis-tris pH 5.5, 50 mM ammonium phosphate and 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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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: May 10, 2013
RadiationMonochromator: Flat graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→34.59 Å / Num. all: 24186 / Num. obs: 24161 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3381 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb id: 3DAI

3dai


Resolution: 1.8→30.93 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.32 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.09 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20494 1235 5.1 %RANDOM
Rwork0.16895 ---
all0.207 24161 --
obs0.17083 22926 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.416 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.12 Å20 Å2
2---0.12 Å20 Å2
3---0.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.8→30.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 43 243 1370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021215
X-RAY DIFFRACTIONr_bond_other_d0.0020.021183
X-RAY DIFFRACTIONr_angle_refined_deg1.6272.0161648
X-RAY DIFFRACTIONr_angle_other_deg0.9423.0052739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7575150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.87223.28467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90315234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5271516
X-RAY DIFFRACTIONr_chiral_restr0.110.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211339
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
X-RAY DIFFRACTIONr_mcbond_it1.7491.767541
X-RAY DIFFRACTIONr_mcbond_other1.7081.761540
X-RAY DIFFRACTIONr_mcangle_it2.7232.627680
X-RAY DIFFRACTIONr_mcangle_other2.7272.632681
X-RAY DIFFRACTIONr_scbond_it2.6482.211674
X-RAY DIFFRACTIONr_scbond_other2.6352.212674
X-RAY DIFFRACTIONr_scangle_other4.1443.192958
X-RAY DIFFRACTIONr_long_range_B_refined9.42418.2911705
X-RAY DIFFRACTIONr_long_range_B_other9.42218.2891705
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 82 -
Rwork0.364 1613 -
obs--94.69 %
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)
114.00681.92244.74861.40460.3575.3681-0.4102-0.62220.8098-0.10170.02440.388-0.1402-0.3150.38580.02420.0325-0.02930.0887-0.02380.1547-6.595945.47116.5092
21.9676-0.9912-0.71780.51080.33471.06050.08920.23730.1349-0.0257-0.0974-0.0529-0.07520.02950.00830.03030.02340.0090.10150.04620.079915.768543.7402-5.717
34.2042-0.1205-1.3340.0611-0.10710.8339-0.11980.3082-0.1211-0.04650.0209-0.0080.1921-0.08370.09890.06070.00680.01720.1061-0.01440.097711.064134.4127-1.2825
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A979 - 987
2X-RAY DIFFRACTION2A988 - 1068
3X-RAY DIFFRACTION3A1069 - 1108

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