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- PDB-1pnr: PURINE REPRESSOR-HYPOXANTHINE-PURF-OPERATOR COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1pnr
TitlePURINE REPRESSOR-HYPOXANTHINE-PURF-OPERATOR COMPLEX
Components
  • DNA (5'-D(*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*TP*TP*TP*TP*CP*GP*T )-3')
  • PROTEIN (PURINE REPRESSOR)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / 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 / 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 domains / 434 Repressor (Amino-terminal Domain) ...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 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: 2.7 Å
AuthorsSchumacher, M.A. / Choi, K.Y. / Zalkin, H. / Brennan, R.G.
CitationJournal: 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
DepositionMar 29, 1995Deposition site: NDB / Processing site: NDB
Revision 1.0Nov 20, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 14, 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(*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*TP*TP*TP*TP*CP*GP*T )-3')
A: PROTEIN (PURINE REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4383
Polymers43,3022
Non-polymers1361
Water82946
1
B: DNA (5'-D(*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*TP*TP*TP*TP*CP*GP*T )-3')
A: PROTEIN (PURINE REPRESSOR)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)86,8766
Polymers86,6044
Non-polymers2722
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)175.850, 94.790, 81.840
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(*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*TP*TP*TP*TP*CP*GP*T )-3')


Mass: 5210.410 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein PROTEIN (PURINE REPRESSOR)


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.: 46 / 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: 68.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2HYPOXANTHINE11
3DTT11
4PHOSPHATE11
5NA CACODYLATE11
6PEG 400011
7NH4 SULFATE11
8[CO(NH3)6]3+11
9NH4 PHOSPHATE11
10WATER12
11PEG 400012
12NH4 SULFATE12
13[CO(NH3)6]3+12
14NH4 PHOSPHATE12
Crystal grow
*PLUS
Details: Schumacher, M.A., (1994) J.Mol.Biol, 242, 302. / pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.5 mMprotein1drop
21.0 mMDTT1drop
3160 mMsodium potassium phosphate1droppH7.4
40.6 mMDNA1drop
550 mMsodium cacodylate1droppH6.9
625 %PEG40001drop
70.4 Mammonium sulfate1drop
850 mMcobalt hexammine1drop
90.1 Mammonium phosphate1droppH7.5
1025 %PEG40001reservoir
110.4 Mammonium sulfate1reservoir
1250 mMcobalt hexammine1reservoir
130.1 Mammonium phosphate1reservoirpH7.5
141

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SDMS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 18242 / % possible obs: 97 % / Observed criterion σ(I): 9.4 / Rmerge(I) obs: 0.056

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.7→10 Å / σ(F): 1 /
RfactorNum. reflection
obs0.171 18242
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 346 10 46 3054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_deg2.4
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
Highest resolution: 2.7 Å / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.4

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