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- PDB-5ulc: PLASMODIUM FALCIPARUM BROMODOMAIN-CONTAINING PROTEIN PF10_0328 -

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Basic information

Entry
Database: PDB / ID: 5ulc
TitlePLASMODIUM FALCIPARUM BROMODOMAIN-CONTAINING PROTEIN PF10_0328
ComponentsBromodomain protein 1
KeywordsSIGNALING PROTEIN / BROMODOMAIN / MALARIA / STRUCTURAL GENOMICS / STRUCTURAL GENOMI CONSORTIUM / SGC
Function / homology
Function and homology information


Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Bromodomain-like / Ankyrin repeat / Histone Acetyltransferase; Chain A / Ankyrin repeat-containing domain superfamily / Bromodomain, conserved site / Bromodomain signature. ...Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Bromodomain-like / Ankyrin repeat / Histone Acetyltransferase; Chain A / Ankyrin repeat-containing domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain protein 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsWernimont, A.K. / Amaya, M.F. / Lam, A. / Ali, A. / Zhang, A.Z. / Kenzina, L. / Lin, Y.H. / MacKenzie, F. / Kozieradzki, I. / Cossar, D. ...Wernimont, A.K. / Amaya, M.F. / Lam, A. / Ali, A. / Zhang, A.Z. / Kenzina, L. / Lin, Y.H. / MacKenzie, F. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Weigelt, J. / Hui, R. / Walker, J.R. / Qiu, W. / Brand, V. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: PLASMODIUM FALCIPARUM BROMODOMAIN-CONTAINING PROTEIN PF10_0328
Authors: Wernimont, A.K. / Amaya, M.F. / Lam, A. / Ali, A. / Zhang, A.Z. / Kenzina, L. / Lin, Y.H. / MacKenzie, F. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / ...Authors: Wernimont, A.K. / Amaya, M.F. / Lam, A. / Ali, A. / Zhang, A.Z. / Kenzina, L. / Lin, Y.H. / MacKenzie, F. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Weigelt, J. / Hui, R. / Walker, J.R. / Qiu, W. / Brand, V. / Structural Genomics Consortium (SGC)
History
DepositionJan 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
SupersessionJan 24, 2018ID: 3FKM
Revision 1.1Jan 24, 2018Group: Advisory / Database references / Structure summary
Category: audit_author / citation_author / pdbx_database_PDB_obs_spr
Item: _audit_author.name / _citation_author.name
Revision 1.2Oct 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 1.3Nov 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
X: Bromodomain protein 1


Theoretical massNumber of molelcules
Total (without water)19,7741
Polymers19,7741
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.603, 88.265, 106.493
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Bromodomain protein 1 / Bromodomain protein / putative


Mass: 19773.770 Da / Num. of mol.: 1 / Fragment: Bromodomain (UNP RESIDUES 333-480)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF10_0328, PF3D7_1033700 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IJ72
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.23 Å3/Da / Density % sol: 44.95 % / Mosaicity: 0.606 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 8% PEG 8000, 0.1 M Tris, Chymotrypsin, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97948 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 6593 / % possible obs: 90.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 45.12 Å2 / Rmerge(I) obs: 0.115 / Χ2: 1.978 / Net I/σ(I): 13.1 / Num. measured all: 42091
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.495.60.1724841.344168.9
2.49-2.595.60.1755041.473172
2.59-2.75.70.1575921.723181.5
2.7-2.855.90.1466382.081189.5
2.85-3.026.10.1286662.163195.6
3.02-3.266.60.1297261.98199.3
3.26-3.5870.1257211.9821100
3.58-4.170.127292.2291100
4.1-5.1770.1127432.081100
5.17-506.60.1027902.148199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RJF

2rjf


Resolution: 2.4→33.98 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.9 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.354 / SU Rfree Blow DPI: 0.226
RfactorNum. reflection% reflectionSelection details
Rfree0.232 305 4.63 %RANDOM
Rwork0.216 ---
obs0.217 6593 90.8 %-
Displacement parametersBiso max: 147.86 Å2 / Biso mean: 66.27 Å2 / Biso min: 44.87 Å2
Baniso -1Baniso -2Baniso -3
1-18.6808 Å20 Å20 Å2
2---30.2557 Å20 Å2
3---11.5749 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.4→33.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 0 33 1003
Biso mean---72.16 -
Num. residues----122
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d436SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes28HARMONIC2
X-RAY DIFFRACTIONt_gen_planes283HARMONIC5
X-RAY DIFFRACTIONt_it1967HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion133SEMIHARMONIC5
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_contact2056SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1967HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3553HARMONIC3.50.58
X-RAY DIFFRACTIONt_omega_torsion2.3
X-RAY DIFFRACTIONt_other_torsion14.69
LS refinement shellResolution: 2.4→2.68 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.232 80 5.41 %
Rwork0.179 1398 -
all0.182 1478 -
obs--73.46 %
Refinement TLS params.Method: refined / Origin x: 33.1642 Å / Origin y: 20.7827 Å / Origin z: 41.1156 Å
111213212223313233
T-0.0953 Å2-0.0137 Å20.0174 Å2-0.18 Å2-0.0157 Å2---0.2349 Å2
L2.0659 °20.1553 °2-0.6612 °2-0.6108 °2-0.2894 °2--2.8273 °2
S0.0094 Å °0.207 Å °-0.1053 Å °0.0453 Å °-0.0449 Å °0.0723 Å °-0.2113 Å °0.0156 Å °0.0354 Å °
Refinement TLS groupSelection details: { X|* }

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