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- PDB-1bdi: PURINE REPRESSOR MUTANT-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1bdi
TitlePURINE REPRESSOR MUTANT-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX
Components
  • DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T )-3')
  • PROTEIN (PURINE REPRESSOR)
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / DNA-BINDING / REPRESSOR / PURINE BIOSYNTHESIS / COMPLEX (DNA-BINDING PROTEIN-DNA) / TRANSCRIPTION-DNA COMPLEX
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 / LacI-type HTH domain signature. / Transcriptional regulator LacI/GalR-like, sensor domain / 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 domains / 434 Repressor (Amino-terminal Domain) ...Transcription regulator HTH, PurR / LacI-type HTH domain signature. / Transcriptional regulator LacI/GalR-like, sensor domain / 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 domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HYPOXANTHINE / DNA / DNA (> 10) / HTH-type transcriptional repressor PurR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsGlasfeld, A. / Schumacher, M.A. / Choi, K.Y. / Zalkin, H. / Brennan, R.G.
Citation
Journal: J.Am.Chem.Soc. / Year: 1996
Title: A Positively Charged Residue Bound in the Minor Groove Does not Alter the Bending of a DNA Duplex
Authors: Glasfeld, A. / Schumacher, M.A. / Choi, K.Y. / Zalkin, H. / Brennan, R.G.
#1: Journal: Science / Year: 1994
Title: Crystal Structure of LacI Member, PurR, Bound to DNA: Minor Groove Binding by Alpha Helices
Authors: Schumacher, M.A. / Choi, K.Y. / Zalkin, H. / Brennan, R.G.
History
DepositionJul 25, 1996Processing site: NDB
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T )-3')
A: PROTEIN (PURINE REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4303
Polymers43,2942
Non-polymers1361
Water362
1
B: DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T )-3')
A: PROTEIN (PURINE REPRESSOR)
hetero molecules

B: DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T )-3')
A: PROTEIN (PURINE REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8606
Polymers86,5884
Non-polymers2722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)176.160, 94.990, 81.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T )-3')


Mass: 5202.384 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein PROTEIN (PURINE REPRESSOR) / PURA


Mass: 38091.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ACP7
#3: Chemical ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.92 Å3/Da / Density % sol: 63 %
Crystal
*PLUS
Density % sol: 63 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.12 mMprotein1drop
20.2 mMdithiothreitol1drop
338 mMsodium-potassium phosphate 1drop
41.7 mMDNA1drop
514.3 mMsodium cacodylate1drop
611.9 %PEG40001drop
70.19 Mammonium sulfate1drop
890 mMcobalt hexammine1drop
90.05 Mammonium phosphate1drop
1025 %PEG40001reservoir
110.4 Mammonium sulphate1reservoir
1250 mMcobalt hexammine1reservoir
130.1 Mammonium phosphate1reservoir

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Data collection

DetectorType: UCSD MARK III / Detector: AREA DETECTOR / Date: Nov 22, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 27051 / % possible obs: 91 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 1.8 % / Rmerge(I) obs: 0.06714
Reflection
*PLUS
% possible obs: 91 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 1.8 %

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Processing

Software
NameClassification
TNTrefinement
UCSDdata reduction
RefinementResolution: 3→10 Å / σ(F): 2 /
RfactorNum. reflection
obs0.157 12428
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 345 10 2 3009
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0140.02
X-RAY DIFFRACTIONt_angle_deg1.72.5
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
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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