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- PDB-1pyi: CRYSTAL STRUCTURE OF A PPR1-DNA COMPLEX: DNA RECOGNITION BY PROTE... -

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Basic information

Entry
Database: PDB / ID: 1pyi
TitleCRYSTAL STRUCTURE OF A PPR1-DNA COMPLEX: DNA RECOGNITION BY PROTEINS CONTAINING A ZN2CYS6 BINUCLEAR CLUSTER
Components
  • DNA (5'-D(*TP*CP*GP*GP*CP*AP*AP*TP*TP*GP*CP*CP*GP*A)-3')
  • PROTEIN (PYRIMIDINE PATHWAY REGULATOR 1)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX / GAL4 / ZINC FINGER / ZN2CYS6 / BINUCLEAR CLUSTER / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


positive regulation of pyrimidine nucleotide biosynthetic process / pyrimidine nucleotide biosynthetic process / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-templated transcription / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Fungal specific transcription factor domain / Zn(2)-C6 fungal-type DNA-binding domain / Transcription factor domain, fungi / Fungal specific transcription factor 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 ...Fungal specific transcription factor domain / Zn(2)-C6 fungal-type DNA-binding domain / Transcription factor domain, fungi / Fungal specific transcription factor 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) / Pyrimidine pathway regulatory protein 1 / Pyrimidine pathway regulatory protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsMarmorstein, R. / Harrison, S.C.
Citation
Journal: Genes Dev. / Year: 1994
Title: Crystal structure of a PPR1-DNA complex: DNA recognition by proteins containing a Zn2Cys6 binuclear cluster.
Authors: Marmorstein, R. / Harrison, S.C.
#1: Journal: Nature / Year: 1992
Title: DNA Recognition by GAL4: Structure of a Protein-DNA Complex
Authors: Marmorstein, R. / Carey, M. / Ptashne, M. / Harrison, S.C.
History
DepositionJan 4, 1995Deposition site: BNL / Processing site: BNL
Revision 1.0Feb 27, 1995Provider: 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 / 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
D: DNA (5'-D(*TP*CP*GP*GP*CP*AP*AP*TP*TP*GP*CP*CP*GP*A)-3')
E: DNA (5'-D(*TP*CP*GP*GP*CP*AP*AP*TP*TP*GP*CP*CP*GP*A)-3')
A: PROTEIN (PYRIMIDINE PATHWAY REGULATOR 1)
B: PROTEIN (PYRIMIDINE PATHWAY REGULATOR 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7378
Polymers30,4754
Non-polymers2624
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.800, 92.600, 174.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: CIS PROLINE - PRO A 49 / 2: CIS PROLINE - PRO B 49

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Components

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


Mass: 4280.792 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein PROTEIN (PYRIMIDINE PATHWAY REGULATOR 1)


Mass: 10956.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YSCPPR1 (ACCESSION X01739) / Plasmid: PRSETA / Cell (production host): BL21 (PLYSS) / Gene (production host): YSCPPR1 (ACCESSION X01739) / Production host: Escherichia coli (E. coli) / References: UniProt: PPR1_YEAST, UniProt: P07272*PLUS
#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.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 55 %
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.6 mMprotein dimer1drop
20.7 mMDNA duplex1drop
37 %PEG35001drop
41 %MPD1drop
587.5 mM1dropNaCl
662.5 mM1dropCaCl2
70.050 mMzinc acetate1drop
80.010 mMsodium cacodylate1droppH6.8
915 %PEG35001reservoir
102 %MPD1reservoir
11125 mM1reservoirCaCl2
120.100 mMzinc acetate1reservoir
1320 mMsodium cacodylate1reservoirpH6.8

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Data collection

DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Oct 9, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 7096 / Observed criterion σ(I): 4 / Redundancy: 4.6 % / Rmerge(I) obs: 0.064
Reflection
*PLUS
Observed criterion σ(I): 4 / Redundancy: 4.6 % / Rmerge(I) obs: 0.064

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Processing

SoftwareName: XDS / Classification: data reduction
RefinementResolution: 3.2→10 Å / σ(F): 0 /
RfactorNum. reflection
Rfree0.33 -
obs0.245 35480
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1253 568 4 1 1826
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 10 Å / σ(F): 0 / Rfactor obs: 0.245 / Rfactor Rfree: 0.33 / Rfactor Rwork: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.017
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg3.7

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