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- PDB-3kde: Crystal structure of the THAP domain from D. melanogaster P-eleme... -

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Basic information

Entry
Database: PDB / ID: 3kde
TitleCrystal structure of the THAP domain from D. melanogaster P-element transposase in complex with its natural DNA binding site
Components
  • 5'-D(*(BRU)P*CP*CP*AP*CP*TP*TP*AP*AP*C)-3'
  • 5'-D(*GP*TP*TP*AP*AP*GP*(BRU)P*GP*GP*A)-3'
  • Transposable element P transposase
KeywordsDNA BINDING PROTEIN/DNA / THAP domain / DNA-binding domain / zinc-finger / beta-alpha-beta / P-element transposase / DNA integration / DNA recombination / DNA-binding / Metal-binding / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


P-element binding / transposase activity / DNA transposition / DNA integration / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / metal ion binding
Similarity search - Function
THAP domain / Herpes Virus-1 / 87kDa Transposase / : / : / : / 87kDa Transposase / TNP-like, RNase H N-terminal domain / TNP-like, GTP-binding insertion domain / TNP-like, RNase H C-terminal domain ...THAP domain / Herpes Virus-1 / 87kDa Transposase / : / : / : / 87kDa Transposase / TNP-like, RNase H N-terminal domain / TNP-like, GTP-binding insertion domain / TNP-like, RNase H C-terminal domain / THAP-type zinc finger superfamily / Zinc finger domain in CG10631, C. elegans LIN-15B and human P52rIPK. / THAP-type zinc finger / THAP domain / Zinc finger THAP-type profile / Other non-globular / Special
Similarity search - Domain/homology
DNA / Transposable element P transposase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.74 Å
AuthorsSabogal, A. / Lyubimov, A.Y. / Berger, J.M. / Rio, D.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves.
Authors: Sabogal, A. / Lyubimov, A.Y. / Corn, J.E. / Berger, J.M. / Rio, D.C.
History
DepositionOct 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 1, 2012Group: Other
Revision 1.3Mar 21, 2012Group: Database references
Revision 1.4Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*GP*TP*TP*AP*AP*GP*(BRU)P*GP*GP*A)-3'
B: 5'-D(*(BRU)P*CP*CP*AP*CP*TP*TP*AP*AP*C)-3'
C: Transposable element P transposase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9694
Polymers14,9043
Non-polymers651
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-10.8 kcal/mol
Surface area7210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.692, 69.325, 35.126
Angle α, β, γ (deg.)90.00, 92.52, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly is a single THAP domain - dsDNA heterodimer

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Components

#1: DNA chain 5'-D(*GP*TP*TP*AP*AP*GP*(BRU)P*GP*GP*A)-3'


Mass: 3188.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic brominated ssDNA oligo
#2: DNA chain 5'-D(*(BRU)P*CP*CP*AP*CP*TP*TP*AP*AP*C)-3'


Mass: 3028.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic brominated ssDNA oligo
#3: Protein Transposable element P transposase / P-element transposase


Mass: 8686.256 Da / Num. of mol.: 1 / Fragment: THAP domain: UNP residues 1-77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: T / Production host: Escherichia coli (E. coli) / References: UniProt: Q7M3K2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: 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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 24% PEG 8000, 5 mM NaCl, 50 mM CAPSO pH 9.0, 10 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2NaCl11
3CAPSO11
4TCEP11
5PEG 800012
6NaCl12
7CAPSO12
8TCEP12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2008
RadiationMonochromator: Si(111) Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. all: 26096 / Num. obs: 26096 / % possible obs: 95 % / Redundancy: 3.5 % / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.049 / Net I/σ(I): 21.6
Reflection shellResolution: 1.74→1.81 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1841 / Rsym value: 0.29 / % possible all: 66.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXAUTOSOLmodel building
REFMAC5.5.0044refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: SAD / Resolution: 1.74→35.09 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU ML: 0.084 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.115 / Stereochemistry target values: Engh & Huber
Details: 1. The Friedel pairs were used in phasing. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS - NOT INCLUDED IN FINAL MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 666 5.1 %RANDOM
Rwork0.17737 ---
obs0.17935 12316 100 %-
all-12316 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 1.74→35.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms567 404 1 107 1079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211063
X-RAY DIFFRACTIONr_bond_other_d0.0010.02615
X-RAY DIFFRACTIONr_angle_refined_deg1.3232.4221519
X-RAY DIFFRACTIONr_angle_other_deg0.84631514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.039579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81423.07726
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05515111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.903155
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02896
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02169
LS refinement shellResolution: 1.74→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 26 -
Rwork0.261 564 -
obs--100 %

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