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- PDB-5vs7: Bromodomain of PF3D7_1475600 from Plasmodium falciparum complexed... -

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Basic information

Entry
Database: PDB / ID: 5vs7
TitleBromodomain of PF3D7_1475600 from Plasmodium falciparum complexed with peptide H4K5ac
Components
  • Bromodomain protein, putative
  • H4K5ac peptide
KeywordsSIGNALING PROTEIN / Bromodomain-acetylated histone complex / Structural Genomics Consortium (SGC)
Function / homology
Function and homology information


Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain protein, putative
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.04 Å
AuthorsHou, C.F.D. / Loppnau, P. / Dong, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Walker, J.R. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Bromodomain of PF3D7_1475600 from Plasmodium falciparum complexed with peptide H4K5ac
Authors: Hou, C.F.D. / Loppnau, P. / Dong, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Walker, J.R. / Structural Genomics Consortium (SGC)
History
DepositionMay 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Oct 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
Revision 1.4Nov 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

Downloads & links

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Assembly

Deposited unit
A: Bromodomain protein, putative
P: H4K5ac peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2064
Polymers15,1362
Non-polymers712
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-24 kcal/mol
Surface area7620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.110, 41.510, 73.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain protein, putative


Mass: 14432.708 Da / Num. of mol.: 1 / Fragment: Bromodomain (UNP residues 8-125)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF14_0724, PF3D7_1475600 / Plasmid: pRARE2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-V3R / References: UniProt: Q8IK82
#2: Protein/peptide H4K5ac peptide


Mass: 702.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: The protein was crystallized at 277K in 25% PEG3350, 0.1 M HEPES pH 7.9, using the vapor diffusion sitting drop method. Final concentration of 2 mM peptide H4K5ac (GRGKacGGK) was added ...Details: The protein was crystallized at 277K in 25% PEG3350, 0.1 M HEPES pH 7.9, using the vapor diffusion sitting drop method. Final concentration of 2 mM peptide H4K5ac (GRGKacGGK) was added directly to the concentrated protein immediately prior to setting up the crystallization plate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97914 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.04→40 Å / Num. obs: 8199 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 46.73 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.031 / Rrim(I) all: 0.08 / Χ2: 0.965 / Net I/σ(I): 7.2 / Num. measured all: 53254
Reflection shellResolution: 2.04→2.08 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.573 / Num. unique obs: 480 / CC1/2: 0.997 / Rpim(I) all: 0.028 / Rrim(I) all: 0.071 / Χ2: 0.892 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NXJ

4nxj


Resolution: 2.04→36.54 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.954 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.249 / SU Rfree Blow DPI: 0.187
RfactorNum. reflection% reflectionSelection details
Rfree0.244 389 4.78 %RANDOM
Rwork0.21 ---
obs0.212 8143 99.2 %-
Displacement parametersBiso max: 119.32 Å2 / Biso mean: 58.82 Å2 / Biso min: 26.72 Å2
Baniso -1Baniso -2Baniso -3
1-6.2593 Å20 Å20 Å2
2---1.8272 Å20 Å2
3----4.432 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 2.04→36.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 2 60 1094
Biso mean--84.21 56.91 -
Num. residues----124
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d471SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes33HARMONIC2
X-RAY DIFFRACTIONt_gen_planes286HARMONIC5
X-RAY DIFFRACTIONt_it2047HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion139SEMIHARMONIC5
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_contact2282SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2055HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3704HARMONIC3.80.67
X-RAY DIFFRACTIONt_omega_torsion3.54
X-RAY DIFFRACTIONt_other_torsion15.68
LS refinement shellResolution: 2.04→2.28 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.344 105 4.75 %
Rwork0.286 2106 -
all0.289 2211 -
obs--97.54 %
Refinement TLS params.Method: refined / Origin x: -4.374 Å / Origin y: 24.2776 Å / Origin z: -2.627 Å
111213212223313233
T-0.206 Å2-0.0222 Å20.025 Å2--0.0669 Å2-0.0414 Å2--0.2358 Å2
L2.1866 °2-0.3297 °20.4902 °2-1.5333 °2-1.0493 °2--2.4475 °2
S-0.0804 Å °0.1829 Å °-0.1613 Å °0.031 Å °0.0267 Å °-0.0189 Å °0.0593 Å °0.0462 Å °0.0537 Å °
Refinement TLS groupSelection details: { A|* }

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