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- PDB-4tz2: Fragment-Based Screening of the Bromodomain of ATAD2 -

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Basic information

Entry
Database: PDB / ID: 4tz2
TitleFragment-Based Screening of the Bromodomain of ATAD2
ComponentsATPase family AAA domain-containing protein 2
KeywordsHydrolase/Hydrolase inhibitor / ATAD2 / Bromodomain / 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
3-(5-phenyl-4H-1,2,4-triazol-3-yl)aniline / ATPase family AAA domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHarner, M.J. / Chauder, B.A. / Phan, J. / Fesik, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)DP1OD006933/DP1CA174419 United States
CitationJournal: J.Med.Chem. / Year: 2014
Title: Fragment-Based Screening of the Bromodomain of ATAD2.
Authors: Harner, M.J. / Chauder, B.A. / Phan, J. / Fesik, S.W.
History
DepositionJul 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)15,9956
Polymers15,4701
Non-polymers5255
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.203, 79.203, 136.036
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-1342-

HOH

21A-1387-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 15469.516 Da / Num. of mol.: 1 / Fragment: UNP residues 981-1108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD / References: UniProt: Q6PL18, EC: 3.6.1.3

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Non-polymers , 5 types, 205 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-39R / 3-(5-phenyl-4H-1,2,4-triazol-3-yl)aniline


Mass: 236.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12N4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Bis-Tris, pH 6.0, 2.2 M (NH4)2SO4, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→38.02 Å / Num. obs: 28313 / % possible obs: 99.9 % / Redundancy: 23.4 % / Rmerge(I) obs: 0.071 / Rsym value: 0.106 / Net I/σ(I): 25.89
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 7.41 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data scaling
MAR345dtbdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DAI

3dai


Resolution: 1.7→38.02 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 2000 7.06 %
Rwork0.169 --
obs0.1713 28309 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→38.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 33 200 1318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191185
X-RAY DIFFRACTIONf_angle_d1.6071610
X-RAY DIFFRACTIONf_dihedral_angle_d19.153472
X-RAY DIFFRACTIONf_chiral_restr0.081175
X-RAY DIFFRACTIONf_plane_restr0.008213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7460.23871390.16571835X-RAY DIFFRACTION100
1.746-1.79320.21451400.15331836X-RAY DIFFRACTION100
1.7932-1.8460.20821400.16881845X-RAY DIFFRACTION100
1.846-1.90560.22211400.16041834X-RAY DIFFRACTION100
1.9056-1.97370.20851400.16911851X-RAY DIFFRACTION100
1.9737-2.05270.21011410.16771842X-RAY DIFFRACTION100
2.0527-2.14610.23131410.15871863X-RAY DIFFRACTION100
2.1461-2.25930.171410.14811849X-RAY DIFFRACTION100
2.2593-2.40080.17351420.15411876X-RAY DIFFRACTION100
2.4008-2.58610.21531420.16231862X-RAY DIFFRACTION100
2.5861-2.84630.20511440.17931895X-RAY DIFFRACTION100
2.8463-3.2580.19291450.17651906X-RAY DIFFRACTION100
3.258-4.10390.19651470.15871942X-RAY DIFFRACTION100
4.1039-38.03260.20231580.18962073X-RAY DIFFRACTION100

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