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- PDB-5tpx: Bromodomain from Plasmodium Faciparum Gcn5, complexed with compound -

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Basic information

Entry
Database: PDB / ID: 5tpx
TitleBromodomain from Plasmodium Faciparum Gcn5, complexed with compound
ComponentsHistone acetyltransferase GCN5
KeywordsTRANSFERASE / Bromodomain / Structural Genomics Consortium (SGC)
Function / homology
Function and homology information


histone H3 acetyltransferase activity / histone acetyltransferase complex / chromatin remodeling / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain profile. / bromo domain / Bromodomain ...Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7H7 / Histone acetyltransferase GCN5
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLin, Y.H. / Hou, C.F.D. / MOUSTAKIM, M. / DIXON, D.J. / Loppnau, P. / Tempel, W. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. ...Lin, Y.H. / Hou, C.F.D. / MOUSTAKIM, M. / DIXON, D.J. / Loppnau, P. / Tempel, W. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / BRENNAN, P.E. / Walker, J.R. / Structural Genomics Consortium (SGC)
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Discovery of a PCAF Bromodomain Chemical Probe.
Authors: Moustakim, M. / Clark, P.G. / Trulli, L. / Fuentes de Arriba, A.L. / Ehebauer, M.T. / Chaikuad, A. / Murphy, E.J. / Mendez-Johnson, J. / Daniels, D. / Hou, C.D. / Lin, Y.H. / Walker, J.R. / ...Authors: Moustakim, M. / Clark, P.G. / Trulli, L. / Fuentes de Arriba, A.L. / Ehebauer, M.T. / Chaikuad, A. / Murphy, E.J. / Mendez-Johnson, J. / Daniels, D. / Hou, C.D. / Lin, Y.H. / Walker, J.R. / Hui, R. / Yang, H. / Dorrell, L. / Rogers, C.M. / Monteiro, O.P. / Fedorov, O. / Huber, K.V. / Knapp, S. / Heer, J. / Dixon, D.J. / Brennan, P.E.
History
DepositionOct 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase GCN5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4506
Polymers14,7661
Non-polymers6845
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.000, 75.000, 49.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-1502-

SO4

21A-1637-

HOH

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Components

#1: Protein Histone acetyltransferase GCN5


Mass: 14765.800 Da / Num. of mol.: 1 / Fragment: Bromodomain (UNP residues 1356-1460)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0823300 / Plasmid: PET15-MHL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3)-pRARE2 / References: UniProt: Q8IB67, histone acetyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-7H7 / (1S,2S)-N~1~,N~1~-dimethyl-N~2~-(3-methyl[1,2,4]triazolo[3,4-a]phthalazin-6-yl)-1-phenylpropane-1,2-diamine


Mass: 360.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.36 Å3/Da / Density % sol: 47.94 % / Mosaicity: 1.537 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The protein was crystallized at 293 K in 0.1M CaCl2, 30% PEG 8K, 0.2M NH4SO4 with 2mM compound using the sitting drop method.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98011 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.1→37.55 Å / Num. obs: 8411 / % possible obs: 96 % / Redundancy: 7.8 % / Biso Wilson estimate: 38.07 Å2 / Rmerge(I) obs: 0.1 / Net I/av σ(I): 20.575 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.1-2.147.80.7250.877189
2.14-2.187.70.7090.847189.4
2.18-2.227.60.6080.911198.6
2.22-2.267.80.4660.934195.3
2.26-2.317.80.440.9511100
2.31-2.377.90.4130.944196.7
2.37-2.427.90.340.956199.5
2.42-2.4980.3070.968196.3
2.49-2.567.80.2890.9661100
2.56-2.6580.2310.981196.4
2.65-2.747.80.2060.986198.1
2.74-2.857.90.170.993198.1
2.85-2.987.90.1350.992196.3
2.98-3.147.90.0970.995196.4
3.14-3.337.90.0780.998196.4
3.33-3.597.90.0750.997196.6
3.59-3.957.80.0810.995196.9
3.95-4.527.80.0650.997193.8
4.52-5.697.70.0520.997195.2
5.69-37.557.10.0560.998192.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
BUSTERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QNS

4qns


Resolution: 2.1→37.5 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.396 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.206 / SU Rfree Blow DPI: 0.18 / SU Rfree Cruickshank DPI: 0.173
RfactorNum. reflection% reflectionSelection details
Rfree0.236 390 4.66 %RANDOM
Rwork0.185 ---
obs0.188 8368 96.1 %-
Displacement parametersBiso max: 102.19 Å2 / Biso mean: 45.42 Å2 / Biso min: 26.88 Å2
Baniso -1Baniso -2Baniso -3
1-6.2745 Å20 Å20 Å2
2--6.2745 Å20 Å2
3----12.5489 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 2.1→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 43 66 979
Biso mean--54.2 48.99 -
Num. residues----106
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d392SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes23HARMONIC2
X-RAY DIFFRACTIONt_gen_planes280HARMONIC5
X-RAY DIFFRACTIONt_it1806HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion120SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2027SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1806HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3250HARMONIC3.80.67
X-RAY DIFFRACTIONt_omega_torsion3.7
X-RAY DIFFRACTIONt_other_torsion14.05
LS refinement shellResolution: 2.1→2.35 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.257 106 4.62 %
Rwork0.182 2188 -
all-2294 -
obs--94.95 %
Refinement TLS params.Method: refined / Origin x: 23.6336 Å / Origin y: 84.979 Å / Origin z: 57.9396 Å
111213212223313233
T-0.183 Å20.0118 Å20.0204 Å2--0.2053 Å2-0.0153 Å2---0.0498 Å2
L2.5974 °20.06 °2-0.0608 °2-1.9328 °2-0.2513 °2--1.8437 °2
S-0.0098 Å °-0.2411 Å °-0.0128 Å °0.2183 Å °-0.012 Å °0.1618 Å °-0.0784 Å °-0.0147 Å °0.0219 Å °
Refinement TLS groupSelection details: { A|* }

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