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- PDB-5u9n: Second Bromodomain of cdg4_1340 from Cryptosporidium parvum, comp... -

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Basic information

Entry
Database: PDB / ID: 5u9n
TitleSecond Bromodomain of cdg4_1340 from Cryptosporidium parvum, complexed with bromosporine
ComponentsBromo domain containing protein
KeywordsSIGNALING PROTEIN / Bromodomain / Ligand / Structural Genomics Consortium (SGC)
Function / homology
Function and homology information


Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromosporine / Bromo domain containing protein
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
Model detailsIn subunit B the protein appears to be significantly disordered, and while some residues in the ...In subunit B the protein appears to be significantly disordered, and while some residues in the range 413-420 have been placed into the density, there is a possibility that the docking is incorrect. The user should use caution in interpreting these results.
AuthorsHou, C.F.D. / Lin, Y.H. / Loppnau, P. / Hutchinson, A. / Dong, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Walker, J.R. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Second Bromodomain of cdg4_1340 from Cryptosporidium parvum, complexed with bromosporine
Authors: Hou, C.F.D. / Lin, Y.H. / Loppnau, P. / Hutchinson, A. / Dong, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Hui, R. / Walker, J.R. / Structural Genomics Consortium (SGC)
History
DepositionDec 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromo domain containing protein
B: Bromo domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6335
Polymers35,7282
Non-polymers9053
Water1,35175
1
A: Bromo domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3643
Polymers17,8641
Non-polymers5012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromo domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2682
Polymers17,8641
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.119, 186.124, 195.176
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Bromo domain containing protein


Mass: 17863.914 Da / Num. of mol.: 2 / Fragment: Second bromodomain (UNP residues 300-450)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (strain Iowa II) (eukaryote)
Strain: Iowa II / Gene: cgd4_1340 / Plasmid: PET15-MHL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3)-V3R-pRARE2 / References: UniProt: Q5CQB7
#2: Chemical ChemComp-BMF / Bromosporine / ethyl (3-methyl-6-{4-methyl-3-[(methylsulfonyl)amino]phenyl}[1,2,4]triazolo[4,3-b]pyridazin-8-yl)carbamate


Mass: 404.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20N6O4S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.95 Å3/Da / Density % sol: 68.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The protein was crystallized at 293 K in 2.5M ammonium sulfate, 0.1 M bis-tris propane pH 7.0. Bromosporine (ethyl (3-methyl-6-{4-methyl-3-[(methylsulfonyl)amino]phenyl}[1,2,4]triazolo[4,3- ...Details: The protein was crystallized at 293 K in 2.5M ammonium sulfate, 0.1 M bis-tris propane pH 7.0. Bromosporine (ethyl (3-methyl-6-{4-methyl-3-[(methylsulfonyl)amino]phenyl}[1,2,4]triazolo[4,3- b]pyridazin-8-yl)carbamate) was added (final concentration of 1 mM)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: 22-ID / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.4→33.67 Å / Num. obs: 22425 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 57.95 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Net I/σ(I): 18 / Num. measured all: 159515 / Scaling rejects: 1179
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.4-2.496.90.6390.8198.6
8.97-33.676.20.0720.995196.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PY6

4py6


Resolution: 2.4→32.54 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.884 / SU R Cruickshank DPI: 0.304 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.209 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.188
Details: In subunit B the protein appears to be significantly disordered, and while some residues in the range 413-420 have been placed into the density, there is a possibility that the docking is ...Details: In subunit B the protein appears to be significantly disordered, and while some residues in the range 413-420 have been placed into the density, there is a possibility that the docking is incorrect. The user should use caution in interpreting these results.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1107 4.95 %RANDOM
Rwork0.225 ---
obs0.226 22371 99.9 %-
Displacement parametersBiso max: 159.17 Å2 / Biso mean: 67.55 Å2 / Biso min: 26.63 Å2
Baniso -1Baniso -2Baniso -3
1--7.7804 Å20 Å20 Å2
2--11.833 Å20 Å2
3----4.0526 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.4→32.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 61 76 2098
Biso mean--92.19 51.25 -
Num. residues----245
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d849SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes630HARMONIC5
X-RAY DIFFRACTIONt_it3912HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion265SEMIHARMONIC5
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_contact4216SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3912HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7003HARMONIC3.80.61
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion16.22
LS refinement shellResolution: 2.4→2.52 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.33 161 5.5 %
Rwork0.291 2768 -
all0.293 2929 -
obs--99.97 %
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)
12.5177-0.69930.19784.8311-0.38012.3122-0.093-0.31790.10740.33830.1378-0.22360.01610.1652-0.0448-0.34180.0557-0.0486-0.1460.0068-0.3611-0.3811217.07205.457
217.3441-1.7510.49742.4579-0.70974.51480.14613.71442.71670.157-0.2766-0.1964-0.1222-0.25790.1306-0.76020.02720.00170.47250.6781-0.29810.476195.686227.938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A303 - 449
2X-RAY DIFFRACTION2{ B|* }B306 - 450

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