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- PDB-1jfs: PURINE REPRESSOR MUTANT-HYPOXANTHINE-PURF OPERATOR COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1jfs
TitlePURINE REPRESSOR MUTANT-HYPOXANTHINE-PURF OPERATOR COMPLEX
Components
  • 5'-D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T)-3'
  • PURINE NUCLEOTIDE SYNTHESIS REPRESSOR
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / DNA-BINDING / REPRESSOR / PURINE BIOSYNTHESIS / COMPLEX (DNA-BINDING PROTEIN-DNA) / ALLOSTERIC REGULATION / 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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHuffman, J.L. / Lu, F. / Zalkin, H. / Brennan, R.G.
CitationJournal: Biochemistry / Year: 2002
Title: Role of residue 147 in the gene regulatory function of the Escherichia coli purine repressor.
Authors: Huffman, J.L. / Lu, F. / Zalkin, H. / Brennan, R.G.
History
DepositionJun 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T)-3'
A: PURINE NUCLEOTIDE SYNTHESIS REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3913
Polymers43,2552
Non-polymers1361
Water55831
1
B: 5'-D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T)-3'
A: PURINE NUCLEOTIDE SYNTHESIS REPRESSOR
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)86,7826
Polymers86,5104
Non-polymers2722
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)176.050, 95.040, 81.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a protein homodimer and duplex oligonucleotide, generated from the protein monomer and single DNA strand in the asymmetric unit by applying the following to chains A, B: 1 1.000000 0.000000 0.000000 0.00000 1 0.000000 1.000000 0.000000 0.00000 1 0.000000 0.000000 1.000000 0.00000 2 1.000000 0.000000 0.000000 0.00000 2 0.000000 -1.000000 0.000000 0.00000 2 0.000000 0.000000 -1.000000 0.00000

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Components

#1: DNA chain 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 PURINE NUCLEOTIDE SYNTHESIS REPRESSOR


Mass: 38052.559 Da / Num. of mol.: 1 / Mutation: W147F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURR / Plasmid: pET24a / 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.: 31 / 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: 68.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, ammonium phosphate, ammonium sulfate, cobalt hexammine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2NH4PO411
3NH4SO411
4Co(NH3)611
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
225 %PEG40001reservoir
30.4 Mammonium sulfate1reservoir
450 mMcobalt hexammine chloride1reservoir
50.1 Mammonium phosphate1reservoirpH7.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: UCSD MARK III / Detector: AREA DETECTOR / Date: Oct 16, 1996
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→10 Å / Num. all: 28721 / Num. obs: 28721 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 34.49 Å2 / Rsym value: 7.54 / Net I/σ(I): 4.84
Reflection shellResolution: 2.9→3.11 Å / Redundancy: 5.28 % / Mean I/σ(I) obs: 1.35 / Num. unique all: 15190 / Rsym value: 20 / % possible all: 97.7
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. obs: 13773 / Num. measured all: 28721 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
Lowest resolution: 3.12 Å / % possible obs: 97.7 % / Rmerge(I) obs: 0.2

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Processing

Software
NameClassification
TNTrefinement
SDMSdata reduction
SDMSdata scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PNR

1pnr


Resolution: 2.9→10 Å / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
obs0.157 93257 97.9 %
all-93257 -
Solvent computationBsol: 47.263 Å2 / ksol: 0.5412 e/Å3
Displacement parametersBiso mean: 4.1 Å2
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2654 345 10 31 3040
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01631011.6
X-RAY DIFFRACTIONt_angle_deg1.75742172.1
X-RAY DIFFRACTIONt_dihedral_angle_d21.34318340
X-RAY DIFFRACTIONt_trig_c_planes0.006676
X-RAY DIFFRACTIONt_gen_planes0.0074156
X-RAY DIFFRACTIONt_it4.10630905.4
X-RAY DIFFRACTIONt_nbd0.03729526
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0066
X-RAY DIFFRACTIONt_plane_restr0.0076

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