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- PDB-1dbq: DNA-BINDING REGULATORY PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1dbq
TitleDNA-BINDING REGULATORY PROTEIN
ComponentsPURINE REPRESSOR
KeywordsDNA-BINDING REGULATORY PROTEIN / TRANSCRIPTION REGULATION / PURINE REPRESSOR
Function / homology
Function and homology information


guanine binding / negative regulation of purine nucleotide biosynthetic process / purine nucleotide biosynthetic process / DNA-binding transcription repressor activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / cytosol
Similarity search - Function
Transcription regulator HTH, PurR / Transcriptional regulator LacI/GalR-like, sensor domain / LacI-type HTH domain signature. / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator ...Transcription regulator HTH, PurR / Transcriptional regulator LacI/GalR-like, sensor domain / LacI-type HTH domain signature. / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional repressor PurR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsSchumacher, M.A. / Choi, K.Y. / Lu, F. / Zalkin, H. / Brennan, R.G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1995
Title: Mechanism of corepressor-mediated specific DNA binding by the purine repressor.
Authors: Schumacher, M.A. / Choi, K.Y. / Lu, F. / Zalkin, H. / Brennan, R.G.
History
DepositionFeb 13, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _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: PURINE REPRESSOR
B: PURINE REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0535
Polymers64,9812
Non-polymers733
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-27 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.040, 125.260, 61.290
Angle α, β, γ (deg.)90.00, 100.17, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAS FOR FULL LENGTH PURINE REPRESSOR, THE COREPRESSOR BINDING DOMAIN IS DIMERIC AND THE ENTRY CONTAINS TWO MONOMERS IN THE ASU. THE CHAIN IDENTIFIERS ARE A AND B.

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Components

#1: Protein PURINE REPRESSOR


Mass: 32490.252 Da / Num. of mol.: 2 / Fragment: COREPRESSOR-FREE COREPRESSOR-BINDING DOMAIN / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ACP7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
220 %PEG6001reservoir
30.1 MTris-HCl1reservoir
40.2 M1reservoirMgCl2

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / Num. obs: 25876 / % possible obs: 88.5 % / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.4 Å / Mean I/σ(I) obs: 3.2

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Processing

SoftwareName: TNT / Classification: refinement
RefinementHighest resolution: 2.2 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.156 -
obs-25876
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4344 0 3 244 4591
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.79
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Rfactor obs: 0.156
Solvent computation
*PLUS
Displacement parameters
*PLUS

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