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- PDB-2er8: Crystal Structure of Leu3 DNA-binding domain complexed with a 12m... -

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Basic information

Entry
Database: PDB / ID: 2er8
TitleCrystal Structure of Leu3 DNA-binding domain complexed with a 12mer DNA duplex
Components
  • 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*G)-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 / MAD / Resolution: 2.85 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 1.3Feb 14, 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_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
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 CHAIN(S). THE 4 BIOLOGICAL MOLECULES CAN BE GENARATED THE FOLLOWING WAY: 1 - CHAIN A, E (RESIDUES 7-12) AND F(RESIDUES 13-18) AND APPYING SYMMETRY 1-X+Y,Y,-Z TO CHAINS C, G (RESIDUES7-12) AND H (RESIDUES 13-18). 2 - CHAIN B, E (RESIDUES 1-16) AND F (RESIDUES 19-24) AND APPYING SYMMETRY 1-Y,1-X,1/3-Z TO CHAINS D, G (RESIDUES 1-6) AND H (RESIDUES 19-24). 3 - CHAIN C, G (RESIDUES 7-12) AND H (RESIDUES 13-18) AND APPYING SYMMETRY 1-X+Y,Y,-Z TO CHAINS A, E (RESIDUES 7-12) AND F (RESIDUES 13-18). 4 - CHAIN D, G (RESIDUES 1-16) AND H (RESIDUES 19-24) AND APPYING SYMMETRY 1-Y,1-X,1/3-Z TO CHAINS B, E (RESIDUES 1-6) AND F (RESIDUES 19-24).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*G)-3'
F: 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*G)-3'
G: 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*G)-3'
H: 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*G)-3'
A: Regulatory protein LEU3
B: Regulatory protein LEU3
C: Regulatory protein LEU3
D: Regulatory protein LEU3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,56516
Polymers49,0428
Non-polymers5238
Water59433
1
E: 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*G)-3'
F: 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*G)-3'
A: Regulatory protein LEU3
B: Regulatory protein LEU3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7838
Polymers24,5214
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*G)-3'
H: 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*G)-3'
C: Regulatory protein LEU3
D: Regulatory protein LEU3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7838
Polymers24,5214
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.500, 107.500, 218.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsOne homodimer bound to DNA is the biologic unit. However, in this case one protein homodimer straddles the ends of two DNA duplexes.

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Components

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


Mass: 3664.380 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein
Regulatory protein LEU3


Mass: 8596.052 Da / Num. of mol.: 4 / Fragment: residues 32-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LEU3 (32-103) / 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.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.67 Å3/Da / Density % sol: 66.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Hepes, 22% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Hepes11
2MPD11
3H2O11
4Hepes12
5MPD12
6H2O12

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Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.2830, 1.2833, 1.2587
DetectorDetector: CCD / Date: Aug 10, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.2831
21.28331
31.25871
ReflectionResolution: 2.85→45 Å / Num. obs: 33071 / % possible obs: 99.9 % / Biso Wilson estimate: 52.9 Å2 / Rsym value: 0.05 / Net I/σ(I): 40.9
Reflection shellHighest resolution: 2.85 Å / Mean I/σ(I) obs: 4.2 / Rsym value: 0.374 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.85→45.53 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 471523.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.265 3116 9.8 %RANDOM
Rwork0.237 ---
obs0.237 31825 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.1012 Å2 / ksol: 0.271521 e/Å3
Displacement parametersBiso mean: 68.7 Å2
Baniso -1Baniso -2Baniso -3
1-12.21 Å20.75 Å20 Å2
2--12.21 Å20 Å2
3----24.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 2.85→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 972 8 33 3032
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.27
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.791.5
X-RAY DIFFRACTIONc_mcangle_it6.462
X-RAY DIFFRACTIONc_scbond_it5.352
X-RAY DIFFRACTIONc_scangle_it8.782.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.391 467 9.6 %
Rwork0.401 4389 -
obs--88.1 %
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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