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- PDB-5ajs: Crystal structure of a coiled-coil domain from human THAP11 -

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Basic information

Entry
Database: PDB / ID: 5ajs
TitleCrystal structure of a coiled-coil domain from human THAP11
ComponentsTHAP DOMAIN-CONTAINING PROTEIN 11
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


regulation of mitochondrial transcription / TORC1 complex / electron transport chain / neuron differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / negative regulation of neuron apoptotic process / cell population proliferation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...regulation of mitochondrial transcription / TORC1 complex / electron transport chain / neuron differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / negative regulation of neuron apoptotic process / cell population proliferation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / cytosol
Similarity search - Function
THAP / Zinc finger domain in CG10631, C. elegans LIN-15B and human P52rIPK. / THAP-type zinc finger / THAP domain / Zinc finger THAP-type profile
Similarity search - Domain/homology
THAP domain-containing protein 11
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCukier, C.D. / Maveyraud, L. / Milon, A. / Gervais, V.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: The C-Terminal Region of the Transcriptional Regulator Thap11 Forms a Parallel Coiled-Coil Domain Involved in Protein Dimerization.
Authors: Cukier, C.D. / Maveyraud, L. / Saurel, O. / Guillet, V. / Milon, A. / Gervais, V.
History
DepositionFeb 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THAP DOMAIN-CONTAINING PROTEIN 11
B: THAP DOMAIN-CONTAINING PROTEIN 11
C: THAP DOMAIN-CONTAINING PROTEIN 11
D: THAP DOMAIN-CONTAINING PROTEIN 11


Theoretical massNumber of molelcules
Total (without water)32,0304
Polymers32,0304
Non-polymers00
Water57632
1
C: THAP DOMAIN-CONTAINING PROTEIN 11
D: THAP DOMAIN-CONTAINING PROTEIN 11


Theoretical massNumber of molelcules
Total (without water)16,0152
Polymers16,0152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-37.4 kcal/mol
Surface area8910 Å2
MethodPISA
2
A: THAP DOMAIN-CONTAINING PROTEIN 11
B: THAP DOMAIN-CONTAINING PROTEIN 11


Theoretical massNumber of molelcules
Total (without water)16,0152
Polymers16,0152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-34.1 kcal/mol
Surface area9230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.757, 39.757, 204.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9969, 0.05653, 0.05395), (-0.0551, -0.9981, 0.02755), (0.0554, 0.02449, 0.9982)97.89, 23.62, -3.154
2given(-0.05142, 0.9986, -0.008135), (0.9986, 0.0515, 0.01087), (0.01127, -0.007565, -0.9999)21.42, -21.18, -0.06357
3given(0.1102, -0.9921, -0.06001), (-0.9939, -0.1095, -0.01439), (0.0077, 0.06123, -0.9981)75.29, 44.04, -2.093

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Components

#1: Protein
THAP DOMAIN-CONTAINING PROTEIN 11


Mass: 8007.538 Da / Num. of mol.: 4 / Fragment: RESIDUES 247-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-20-THAP11 (201-314) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96EK4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Description: THE COILED-COIL PART OF THE ENTRY 1N6M - AMINO- ACIDS 300-345 - WAS USED AS A SEARCH MODEL.
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1 M NA/K PHOSPHATE PH 6.2, 0.2 M NACL, 40% (V/V) MPD, HANGING DROP VAPOUR DIFFUSION, T = 285 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2014 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.508
11-H, K, -L20.492
ReflectionResolution: 2.3→39.76 Å / Num. obs: 13992 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 52.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.6 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N6M

1n6m


Resolution: 2.3→39.76 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.336 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29516 737 5.3 %THIN SHELLS
Rwork0.207 ---
obs0.21236 13209 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 78.591 Å2
Baniso -1Baniso -2Baniso -3
1-32.55 Å20 Å20 Å2
2--32.55 Å20 Å2
3----65.09 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 0 32 1912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191905
X-RAY DIFFRACTIONr_bond_other_d0.0010.021945
X-RAY DIFFRACTIONr_angle_refined_deg1.7082.0082550
X-RAY DIFFRACTIONr_angle_other_deg0.82734410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7755250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25122.16274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.13415389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8481525
X-RAY DIFFRACTIONr_chiral_restr0.0780.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022104
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02397
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.588.0421003
X-RAY DIFFRACTIONr_mcbond_other7.5828.0381002
X-RAY DIFFRACTIONr_mcangle_it9.98912.0061249
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.98.598902
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.116 1 -
Rwork0.237 1031 -
obs--97.82 %

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