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- PDB-2czr: Crystal structure of TBP-interacting protein (Tk-TIP26) and impli... -

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Basic information

Entry
Database: PDB / ID: 2czr
TitleCrystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA
ComponentsTBP-interacting protein
KeywordsTRANSCRIPTION REGULATOR / TATA-binding protein (TBP) / TBP-interacting protein (TIP) / hyperthermophilic archaeon / Zn-finger motif
Function / homology
Function and homology information


TBP-interacting protein, N-terminal domain / TBP-interacting protein, C-terminal domain / TBP-interacting protein, N-terminal / TBP-interacting protein, N-terminal superfamily / TBP-interacting protein, C-terminal / TBP-interacting protein N-terminus / Trna Endonuclease; Chain: A, domain 1 / Nucleoside Triphosphate Pyrophosphohydrolase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / TBP-interacting protein
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsYamamoto, T. / Matsuda, T. / Inoue, T. / Matsumura, H. / Morikawa, M. / Kanaya, S. / Kai, Y.
CitationJournal: Protein Sci. / Year: 2006
Title: Crystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA
Authors: Yamamoto, T. / Matsuda, T. / Inoue, T. / Matsumura, H. / Morikawa, M. / Kanaya, S. / Kai, Y.
History
DepositionJul 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: TBP-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1564
Polymers25,9061
Non-polymers2503
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TBP-interacting protein
hetero molecules

A: TBP-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3128
Polymers51,8122
Non-polymers4996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_464y-1,x+1,-z-11
Buried area5100 Å2
ΔGint-15 kcal/mol
Surface area21430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)73.834, 73.834, 86.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein TBP-interacting protein


Mass: 25906.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)pLysS / References: GenBank: 57159431, UniProt: Q9V2W6*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG8000, MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL40B210.9793, 0.9795, 0.9873
SYNCHROTRONSPring-8 BL41XU20.9686
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 17, 2001
MAR CCD 165 mm2CCDOct 14, 2001
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
30.98731
40.96861
ReflectionResolution: 2.3→40 Å / Biso Wilson estimate: 32.7 Å2
Reflection shellResolution: 2.3→2.42 Å

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→36.92 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 452732.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 996 10.3 %RANDOM
Rwork0.191 ---
obs0.191 9652 87.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.2319 Å2 / ksol: 0.369352 e/Å3
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2--1.93 Å20 Å2
3----3.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→36.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 13 110 1954
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.472
X-RAY DIFFRACTIONc_scbond_it2.222
X-RAY DIFFRACTIONc_scangle_it3.412.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 130 9.2 %
Rwork0.226 1286 -
obs--78.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5gll.paramgll.top

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