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- PDB-4py6: Crystal Structure of bromodomain of PFA0510w from Plasmodium Falc... -

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Basic information

Entry
Database: PDB / ID: 4py6
TitleCrystal Structure of bromodomain of PFA0510w from Plasmodium Falciparum
ComponentsBromodomain protein, putative
KeywordsPROTEIN BINDING / Structural Genomics / Structural Genomics Consortium / SGC / bromodomain / malaria
Function / homology
Function and homology information


: / NuA4 histone acetyltransferase complex
Similarity search - Function
Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-R78 / Bromodomain protein, putative
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsFonseca, M. / Tallant, C. / Hutchinson, A. / Savitsky, P. / Krojer, T. / Filippakopoulos, P. / Loppnau, P. / Brennan, P.E. / von Delft, F. / Dong, A. ...Fonseca, M. / Tallant, C. / Hutchinson, A. / Savitsky, P. / Krojer, T. / Filippakopoulos, P. / Loppnau, P. / Brennan, P.E. / von Delft, F. / Dong, A. / Josling, G.A. / Duffy, M.F. / Arrowsmith, C.H. / Bountra, C. / Hui, R. / Knapp, S. / Wernimont, A.K. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of bromodomain of PFA0510w from Plasmodium Falciparum
Authors: Fonseca, M. / Tallant, C. / Hutchinson, A. / Savitsky, P. / Krojer, T. / Filippakopoulos, P. / Loppnau, P. / Brennan, P.E. / von Delft, F. / Dong, A. / Josling, G.A. / Duffy, M.F. / ...Authors: Fonseca, M. / Tallant, C. / Hutchinson, A. / Savitsky, P. / Krojer, T. / Filippakopoulos, P. / Loppnau, P. / Brennan, P.E. / von Delft, F. / Dong, A. / Josling, G.A. / Duffy, M.F. / Arrowsmith, C.H. / Bountra, C. / Hui, R. / Knapp, S. / Wernimont, A.K. / Structural Genomics Consortium (SGC)
History
DepositionMar 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Structure summary
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Bromodomain protein, putative
B: Bromodomain protein, putative
C: Bromodomain protein, putative
D: Bromodomain protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,09611
Polymers69,8234
Non-polymers2,2737
Water2,414134
1
A: Bromodomain protein, putative
C: Bromodomain protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0175
Polymers34,9122
Non-polymers1,1053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-8 kcal/mol
Surface area16040 Å2
MethodPISA
2
B: Bromodomain protein, putative
D: Bromodomain protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0796
Polymers34,9122
Non-polymers1,1674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-8 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.324, 84.269, 219.724
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
DetailsAUTHORS HAVE INDICATED THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein
Bromodomain protein, putative


Mass: 17455.848 Da / Num. of mol.: 4 / Fragment: unp residues 1172-1315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PFA0510w, PFA_0510w, PFUGPA_00085 / Plasmid: pET15-MHL / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q8I240
#2: Chemical
ChemComp-R78 / 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide


Mass: 521.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H39N7O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, 0.1 M CaCl2, 20% PEG6k, 15% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.33→29.41 Å / Num. all: 29997 / Num. obs: 29757 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 49.19 Å2 / Rmerge(I) obs: 0.164 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.33-2.416.10.5612.516604272993.5
9.02-29.415.50.0619.7312656796.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.2.17data scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.41 Å / Cor.coef. Fo:Fc: 0.8798 / Cor.coef. Fo:Fc free: 0.8581 / SU R Cruickshank DPI: 0.556 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 1254 5.16 %RANDOM
Rwork0.237 ---
obs0.2387 24293 99.77 %-
all-24349 --
Displacement parametersBiso max: 117.09 Å2 / Biso mean: 45.17 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--7.215 Å20 Å20 Å2
2--12.7126 Å20 Å2
3----5.4976 Å2
Refine analyzeLuzzati coordinate error obs: 0.444 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 128 134 4686
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1716SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes160HARMONIC2
X-RAY DIFFRACTIONt_gen_planes631HARMONIC5
X-RAY DIFFRACTIONt_it4708HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion592SEMIHARMONIC5
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_contact5336SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4708HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg6344HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion1.6
X-RAY DIFFRACTIONt_other_torsion19.95
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3013 150 5.12 %
Rwork0.2831 2782 -
all0.284 2932 -
obs--99.77 %
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)
13.0514-0.6182-0.25351.5902-0.02121.74950.0327-0.15540.0950.0146-0.069-0.0639-0.05390.25490.0363-0.1734-0.0250.01750.12650.0368-0.1393-24.611-33.005-42.367
21.4343-0.8738-0.31732.69910.17212.1912-0.00170.0102-0.10650.0432-0.09130.29790.2905-0.01670.093-0.1975-0.08890.02610.17380.0139-0.1636-18.612-28.669-68.071
31.38230.05120.27863.01680.30172.42320.0103-0.04030.00890.0392-0.0892-0.2379-0.02870.15960.079-0.3036-0.0191-0.0370.3040.0671-0.2788-23.935-33.878-14.584
42.78240.8361-0.68891.1925-0.36682.9288-0.09970.38250.0251-0.13710.09830.10640.3281-0.54420.0014-0.2083-0.0934-0.00630.304-0.0514-0.304-18.679-28.482-95.703
51.2277-0.9919-2.88310-1.84911.4275-0.0083-0.1224-0.02050.0059-0.03740.03140.03380.07530.0458-0.07190.0158-0.03140.12370.0669-0.2834-17.251-33.009-52.394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1186 - A|1317 }A1186 - 1317
2X-RAY DIFFRACTION2{ B|1188 - B|1318 }B1188 - 1318
3X-RAY DIFFRACTION3{ C|1190 - C|1316 }C1190 - 1316
4X-RAY DIFFRACTION4{ D|1191 - D|1318 }D1191 - 1318
5X-RAY DIFFRACTION5{ A|1401 - A|1401 C|1401 - C|1401 B|1401 - B|1401 D|1401 - D|1401 }A1401
6X-RAY DIFFRACTION5{ A|1401 - A|1401 C|1401 - C|1401 B|1401 - B|1401 D|1401 - D|1401 }C1401
7X-RAY DIFFRACTION5{ A|1401 - A|1401 C|1401 - C|1401 B|1401 - B|1401 D|1401 - D|1401 }B1401
8X-RAY DIFFRACTION5{ A|1401 - A|1401 C|1401 - C|1401 B|1401 - B|1401 D|1401 - D|1401 }D1401

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