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- PDB-2ere: Crystal Structure of a Leu3 DNA-binding domain complexed with a 1... -

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Basic information

Entry
Database: PDB / ID: 2ere
TitleCrystal Structure of a Leu3 DNA-binding domain complexed with a 15mer DNA duplex
Components
  • 5'-D(*TP*TP*GP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*CP*A)-3'
  • Regulatory protein LEU3
KeywordsTRANSCRIPTION ACTIVATOR/DNA / Zn(2)Cys(6)Binuclear Cluster Motif / TRANSCRIPTION ACTIVATOR-DNA COMPLEX
Function / homology
Function and homology information


positive regulation of L-leucine biosynthetic process / L-leucine biosynthetic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II ...positive regulation of L-leucine biosynthetic process / L-leucine biosynthetic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Zn(2)-C6 fungal-type DNA-binding domain / CD2-Gal4 / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA (> 10) / Regulatory protein LEU3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFitzgerald, M.X. / Marmorstein, R.
CitationJournal: Structure / Year: 2006
Title: Structure of a Leu3-DNA complex: recognition of everted CGG half-sites by a Zn2Cys6 binuclear cluster protein.
Authors: Fitzgerald, M.X. / Rojas, J.R. / Kim, J.M. / Kohlhaw, G.B. / Marmorstein, R.
History
DepositionOct 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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
C: 5'-D(*TP*TP*GP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*CP*A)-3'
D: 5'-D(*TP*TP*GP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*CP*A)-3'
A: Regulatory protein LEU3
B: Regulatory protein LEU3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6268
Polymers26,3644
Non-polymers2624
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.565, 66.565, 122.768
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
DetailsAsymmetric unit contains one biologic unit with a homodimer of protein bound to DNA.

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Components

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


Mass: 4585.972 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Regulatory protein LEU3


Mass: 8596.052 Da / Num. of mol.: 2 / Fragment: residues 32-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LEU3 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P08638
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.93 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM Cacodylate, 200 mM NH4OAc, 10 mM CaCl2, 5% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1CacodylateCacodylic acid11
2PEG 400011
3NH4OAc11
4CaCl211
5H2O11
6CacodylateCacodylic acid12
7NH4OAc12
8CaCl212
9PEG 400012
10H2O12

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9213 Å
DetectorDetector: CCD / Date: Jun 8, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9213 Å / Relative weight: 1
ReflectionResolution: 3→32 Å / Num. obs: 6131 / % possible obs: 98.3 % / Rsym value: 0.0793 / Net I/σ(I): 4.8
Reflection shellHighest resolution: 3 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.126 / % possible all: 98.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: One biological unit of pdb entry 2ER8

2er8


Resolution: 3→32.12 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 510996.42 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.277 626 10.3 %RANDOM
Rwork0.277 ---
obs0.277 6101 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 159.103 Å2 / ksol: 0.433733 e/Å3
Displacement parametersBiso mean: 90.1 Å2
Baniso -1Baniso -2Baniso -3
1-23.07 Å212.22 Å20 Å2
2--23.07 Å20 Å2
3----46.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 3→32.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 608 4 24 1506
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.496 114 11 %
Rwork0.423 925 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water_rep.param

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