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- PDB-4ldf: Crystal Structure of CpBRD2 from cryptosporidium, cgd3_3190 -

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Basic information

Entry
Database: PDB / ID: 4ldf
TitleCrystal Structure of CpBRD2 from cryptosporidium, cgd3_3190
ComponentsGCN5 like acetylase + bromodomain
KeywordsTRANSFERASE / Structural Genomics Consortium / SGC / bromodomain
Function / homology
Function and homology information


histone acetyltransferase activity / 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 / Bromodomain profile. / bromo domain ...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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
GCN5 like acetylase + bromodomain
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsWernimont, A.K. / Loppnau, P. / Fonseca, M. / Knapp, S. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Mottaghi, K. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of CpBRD2 from cryptosporidium, cgd3_3190
Authors: Wernimont, A.K. / Loppnau, P. / Fonseca, M. / Knapp, S. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Mottaghi, K.
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
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: GCN5 like acetylase + bromodomain
B: GCN5 like acetylase + bromodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7755
Polymers27,5912
Non-polymers1843
Water1,928107
1
A: GCN5 like acetylase + bromodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8882
Polymers13,7961
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GCN5 like acetylase + bromodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8883
Polymers13,7961
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: GCN5 like acetylase + bromodomain
hetero molecules

B: GCN5 like acetylase + bromodomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7755
Polymers27,5912
Non-polymers1843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_758-x+2,y+1/2,-z+31
Buried area1750 Å2
ΔGint-10 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.892, 44.642, 59.537
Angle α, β, γ (deg.)90.000, 96.500, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein GCN5 like acetylase + bromodomain


Mass: 13795.596 Da / Num. of mol.: 2 / Fragment: unp residue 541-655
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: cgd3_3190 / Plasmid: pet15mlh / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CUE2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 1.81 Å3/Da / Density % sol: 32.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30 % PEG 2K MME 0.1 M Potassium thiocyanate 15% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 13570 / Num. obs: 13557 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.118 / Χ2: 1.536 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.033.30.7566711.183199.4
2.03-2.073.30.6976601.19199.7
2.07-2.113.40.6036961.206199.7
2.11-2.153.40.4956461.3199.7
2.15-2.23.40.4696751.338199.9
2.2-2.253.40.3856801.3321100
2.25-2.313.40.3516651.47199.8
2.31-2.373.40.2986811.4751100
2.37-2.443.40.2636621.5641100
2.44-2.523.50.2456791.4411100
2.52-2.613.40.2316641.5221100
2.61-2.713.50.1966911.4841100
2.71-2.843.50.1566731.6531100
2.84-2.993.50.1296851.5761100
2.99-3.173.50.1016761.6651100
3.17-3.423.50.0786771.7371100
3.42-3.763.50.0566901.6991100
3.76-4.313.50.0456771.6541100
4.31-5.433.50.0497031.8331100
5.43-503.40.0527062.278199

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å33.53 Å
Translation2 Å33.53 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.1phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→33.53 Å / Cor.coef. Fo:Fc: 0.9214 / Cor.coef. Fo:Fc free: 0.8924 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 670 4.96 %RANDOM
Rwork0.1844 ---
all0.1864 13536 --
obs0.1864 13518 99.86 %-
Displacement parametersBiso max: 81.53 Å2 / Biso mean: 25.2892 Å2 / Biso min: 6.2 Å2
Baniso -1Baniso -2Baniso -3
1--11.0241 Å20 Å20.9346 Å2
2--8.7506 Å20 Å2
3---2.2735 Å2
Refine analyzeLuzzati coordinate error obs: 0.215 Å
Refinement stepCycle: LAST / Resolution: 2→33.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 13 107 1875
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d654SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes261HARMONIC5
X-RAY DIFFRACTIONt_it1847HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion246SEMIHARMONIC5
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_contact2328SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1847HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2504HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion17.18
LS refinement shellResolution: 2→2.16 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2399 149 5.42 %
Rwork0.2085 2601 -
all0.2103 2750 -
obs--99.86 %

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