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- PDB-1qp4: PURINE REPRESSOR-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1qp4
TitlePURINE REPRESSOR-HYPOXANTHINE-PALINDROMIC OPERATOR COMPLEX
Components
  • DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*TP*CP*GP*AP*TP*TP*GP*CP*GP*T)-3')
  • PROTEIN (PURINE NUCLEOTIDE SYNTHESIS 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. / Koehler, A.N. / Schumacher, M.A. / Brennan, R.G.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions.
Authors: Glasfeld, A. / Koehler, A.N. / Schumacher, M.A. / 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
DepositionJun 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
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
M: DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*TP*CP*GP*AP*TP*TP*GP*CP*GP*T)-3')
A: PROTEIN (PURINE NUCLEOTIDE SYNTHESIS REPRESSOR)
hetero molecules


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

M: DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*TP*CP*GP*AP*TP*TP*GP*CP*GP*T)-3')
A: PROTEIN (PURINE NUCLEOTIDE SYNTHESIS 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)176.480, 95.260, 81.180
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*TP*CP*GP*AP*TP*TP*GP*CP*GP*T)-3') / PURA


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


Mass: 38091.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURR / Plasmid: PDNA100\:K55A / Gene (production host): PURR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 LAMBDA DE3 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, (NH4)2SO4, [CO(NH3)6]CL3, NA2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1[CO(NH3)6]CL311
2(NH4)2SO411
3NA2SO411
4PEG 400011
5(NH4)2SO412
6NA2SO412
7PEG 400012
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 mMprotein1drop
21.0 mMdithiothreitol1drop
3160 mMsodium potassium phosphate1drop
40.6 mMDNA1drop
550 mMsodium cacodylate1drop
625 %PEG40001drop
70.4 %ammonium sulfate1drop
850 mMcobalt hexammine1drop
90.1 Mammonium phosphate1drop
1025 %PEG40001reservoir
110.4 Mammonium sulphate1reservoir
1250 mMcobalt hexammine1reservoir
130.1 Mammonium phosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: UCSD MARK III / Detector: AREA DETECTOR / Date: Feb 14, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→10 Å / Num. obs: 13547 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 41 Å2 / Rsym value: 7.97 / Net I/σ(I): 9.32
Reflection shellResolution: 3→3.23 Å / Redundancy: 1.8 % / % possible all: 89.6
Reflection
*PLUS
Num. measured all: 58105 / Rmerge(I) obs: 0.0797
Reflection shell
*PLUS
% possible obs: 89.6 %

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Processing

Software
NameClassification
TNTrefinement
UCSD-systemdata reduction
UCSD-systemdata scaling
RefinementResolution: 3→10 Å / σ(I): 2
Stereochemistry target values: DNA BASE GEOMETRIES TAKEN FROM CLOWNEY ET AL. (1996) J. AM. CHEM. SOC., VOL. 118, PP. 509-518. SUGAR PHOSPHATE GEOMETRIES TAKEN FROM GELBIN ET AL. (1996) J. AM. CHEM. ...Stereochemistry target values: DNA BASE GEOMETRIES TAKEN FROM CLOWNEY ET AL. (1996) J. AM. CHEM. SOC., VOL. 118, PP. 509-518. SUGAR PHOSPHATE GEOMETRIES TAKEN FROM GELBIN ET AL. (1996) J. AM. CHEM. SOC., VOL. 118, PP. 519-529.
RfactorNum. reflection
all0.157 -
obs-13547
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_d0.0152.1
X-RAY DIFFRACTIONt_angle_deg1.81.8
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

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