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- PDB-1tf6: CO-CRYSTAL STRUCTURE OF XENOPUS TFIIIA ZINC FINGER DOMAIN BOUND T... -

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Basic information

Entry
Database: PDB / ID: 1tf6
TitleCO-CRYSTAL STRUCTURE OF XENOPUS TFIIIA ZINC FINGER DOMAIN BOUND TO THE 5S RIBOSOMAL RNA GENE INTERNAL CONTROL REGION
Components
  • DNA (5'-D(*AP*CP*GP*GP*GP*CP*CP*TP*GP*GP*TP*TP*AP*GP*TP*AP*C P*CP*TP*GP*GP*AP* TP*GP*GP*GP*AP*GP*AP*CP*C)-3')
  • DNA (5'-D(*TP*GP*GP*TP*CP*TP*CP*CP*CP*AP*TP*CP*CP*AP*GP*GP*T P*AP*CP*TP*AP*AP* CP*CP*AP*GP*GP*CP*CP*CP*G)-3')
  • PROTEIN (TRANSCRIPTION FACTOR IIIA)
KeywordsTRANSCRIPTION/DNA / COMPLEX (TRANSCRIPTION REGULATION-DNA) / RNA POLYMERASE III / TRANSCRIPTION INITIATION / ZINC FINGER PROTEIN / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


ribosomal large subunit biogenesis / DNA binding / RNA binding / metal ion binding / nucleus
Similarity search - Function
Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor IIIA
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.1 Å
AuthorsNolte, R.T. / Conlin, R.M. / Harrison, S.C. / Brown, R.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex.
Authors: Nolte, R.T. / Conlin, R.M. / Harrison, S.C. / Brown, R.S.
History
DepositionMar 2, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 10, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
B: DNA (5'-D(*AP*CP*GP*GP*GP*CP*CP*TP*GP*GP*TP*TP*AP*GP*TP*AP*C P*CP*TP*GP*GP*AP* TP*GP*GP*GP*AP*GP*AP*CP*C)-3')
C: DNA (5'-D(*TP*GP*GP*TP*CP*TP*CP*CP*CP*AP*TP*CP*CP*AP*GP*GP*T P*AP*CP*TP*AP*AP* CP*CP*AP*GP*GP*CP*CP*CP*G)-3')
E: DNA (5'-D(*AP*CP*GP*GP*GP*CP*CP*TP*GP*GP*TP*TP*AP*GP*TP*AP*C P*CP*TP*GP*GP*AP* TP*GP*GP*GP*AP*GP*AP*CP*C)-3')
F: DNA (5'-D(*TP*GP*GP*TP*CP*TP*CP*CP*CP*AP*TP*CP*CP*AP*GP*GP*T P*AP*CP*TP*AP*AP* CP*CP*AP*GP*GP*CP*CP*CP*G)-3')
A: PROTEIN (TRANSCRIPTION FACTOR IIIA)
D: PROTEIN (TRANSCRIPTION FACTOR IIIA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,17418
Polymers82,3896
Non-polymers78512
Water0
1
B: DNA (5'-D(*AP*CP*GP*GP*GP*CP*CP*TP*GP*GP*TP*TP*AP*GP*TP*AP*C P*CP*TP*GP*GP*AP* TP*GP*GP*GP*AP*GP*AP*CP*C)-3')
C: DNA (5'-D(*TP*GP*GP*TP*CP*TP*CP*CP*CP*AP*TP*CP*CP*AP*GP*GP*T P*AP*CP*TP*AP*AP* CP*CP*AP*GP*GP*CP*CP*CP*G)-3')
A: PROTEIN (TRANSCRIPTION FACTOR IIIA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5879
Polymers41,1953
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*AP*CP*GP*GP*GP*CP*CP*TP*GP*GP*TP*TP*AP*GP*TP*AP*C P*CP*TP*GP*GP*AP* TP*GP*GP*GP*AP*GP*AP*CP*C)-3')
F: DNA (5'-D(*TP*GP*GP*TP*CP*TP*CP*CP*CP*AP*TP*CP*CP*AP*GP*GP*T P*AP*CP*TP*AP*AP* CP*CP*AP*GP*GP*CP*CP*CP*G)-3')
D: PROTEIN (TRANSCRIPTION FACTOR IIIA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5879
Polymers41,1953
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.180, 64.712, 78.035
Angle α, β, γ (deg.)90.07, 92.98, 102.95
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.90069, -0.43447, 0.00204), (-0.43444, 0.90067, 0.00782), (-0.00524, 0.00616, -0.99997)78.54161, 18.46218, 82.12378
2given(-0.89683, -0.44229, -0.00873), (-0.44235, 0.89681, 0.00772), (0.00442, 0.01079, -0.99993)78.89021, 18.84468, 81.35723
3given(-0.89287, -0.45031, -0.00028), (-0.45031, 0.89286, 0.0051), (-0.00205, 0.00467, -0.99999)78.95392, 19.75191, 82.6093
4given(-0.89242, -0.4512, -0.0024), (-0.45121, 0.89241, 0.00452), (0.0001, 0.00511, -0.99999)79.06322, 19.84412, 82.49853

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Components

#1: DNA chain DNA (5'-D(*AP*CP*GP*GP*GP*CP*CP*TP*GP*GP*TP*TP*AP*GP*TP*AP*C P*CP*TP*GP*GP*AP* TP*GP*GP*GP*AP*GP*AP*CP*C)-3') / 5S RIBOSOMAL RNA GENE


Mass: 9634.182 Da / Num. of mol.: 2 / Fragment: INTERNAL PROMOTER REGION / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*GP*GP*TP*CP*TP*CP*CP*CP*AP*TP*CP*CP*AP*GP*GP*T P*AP*CP*TP*AP*AP* CP*CP*AP*GP*GP*CP*CP*CP*G)-3') / 5S RIBOSOMAL RNA GENE


Mass: 9434.062 Da / Num. of mol.: 2 / Fragment: INTERNAL PROMOTER REGION / Source method: obtained synthetically
#3: Protein PROTEIN (TRANSCRIPTION FACTOR IIIA) / TRANSCRIPTION FACTOR IIIA


Mass: 22126.504 Da / Num. of mol.: 2 / Fragment: NH2-TERMINAL SIX FINGERS, RESIDUE 1-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Description: CDNA; / Cell: OOCYTE / Organ: OVARY / Organelle: NUCLEUSCell nucleus / Plasmid: PRSET B / Species (production host): Escherichia coli / Cellular location (production host): INCLUSION BODY / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03001
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 70 %
Description: DATA WERE FILTERED LOCALLY WITH AN I/SIGMA(I) CUTOFF OF 1.0 - ELIMINATION OF UNRELIABLE MEASUREMENTS.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: COMPLEX WAS CRYSTALLIZED FROM 22.5% PEG 4000, 165 MM NACL, 35 MM SODIUM ACETATE, 3.2 MM DTT, 9.2% (VOL/VOL) GLYCEROL, 1.8 MM NAN3, 1.8 MM CADAVERINE-2HCL, 5.5 MM TRIS-HCL, PH 8.0, VAPOR ...Details: COMPLEX WAS CRYSTALLIZED FROM 22.5% PEG 4000, 165 MM NACL, 35 MM SODIUM ACETATE, 3.2 MM DTT, 9.2% (VOL/VOL) GLYCEROL, 1.8 MM NAN3, 1.8 MM CADAVERINE-2HCL, 5.5 MM TRIS-HCL, PH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NACLSodium chloride11
3SODIUM ACETATE11
4DTT11
5GLYCEROL11
6NAN311
7CADAVERINE-2HCL11
8TRIS-HCLTris11
9PEG 400011
10WATER12
11PEG 400012

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 19034 / % possible obs: 77.4 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.128 / Rsym value: 0.06
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 25 Å / % possible obs: 77.4 % / Num. measured all: 126746

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Processing

Software
NameVersionClassification
CCP4RAVE DMmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RAVEphasing
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 3.1→8 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: ISOTROPIC B FACTORS WERE REFINED AGAINST UNSHARPENED NATIVE DATA WHICH HAS AN INHERENT B FACTOR OF 65.0, AND R-FACTORS WERE CALCULATED USING ANISOTROPICALLY SHARPENED DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.363 497 2.9 %RANDOM
Rwork0.308 ---
obs0.308 17014 81.4 %-
Displacement parametersBiso mean: 65 Å2
Baniso -1Baniso -2Baniso -3
1-17.26 Å24.52 Å2-0.72 Å2
2---5.82 Å21.02 Å2
3----11.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.64 Å0.55 Å
Luzzati d res low-8 Å
Luzzati sigma a-0.43 Å
Refinement stepCycle: LAST / Resolution: 3.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2953 2530 12 0 5495
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.94
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.472
X-RAY DIFFRACTIONx_mcangle_it4.454
X-RAY DIFFRACTIONx_scbond_it2.492
X-RAY DIFFRACTIONx_scangle_it4.484
Refine LS restraints NCSNCS model details: NONE
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM_NDBX.DNATOP_NBDX.DNA
X-RAY DIFFRACTION3PARAM19.IONTOPH19.ION
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 2.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 65 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg0.9
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.94
X-RAY DIFFRACTIONx_mcbond_it2.472
X-RAY DIFFRACTIONx_scbond_it2.492
X-RAY DIFFRACTIONx_mcangle_it4.454
X-RAY DIFFRACTIONx_scangle_it4.484

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