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- PDB-2pua: CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: ... -

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Basic information

Entry
Database: PDB / ID: 2pua
TitleCRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES
Components
  • DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T )-3')
  • PURINE REPRESSOR
KeywordsTRANSCRIPTION/DNA / COMPLEX (DNA-BINDING PROTEIN-DNA) / DNA-BINDING REGULATORY PROTEIN / 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
6-METHYLPURINE / DNA / DNA (> 10) / HTH-type transcriptional repressor PurR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsSchumacher, R.G. / Choi, K.Y. / Zalkin, H. / Brennan, M.A.
Citation
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.
#1: Journal: Biochemistry / Year: 1998
Title: Structure-Based Redesign of Corepressor Specificity of the Escherichia Coli Purine Repressor by Substitution of Residue 190
Authors: Lu, F. / Schumacher, M.A. / Arvidson, D.N. / Haldimann, A. / Wanner, B.L. / Zalkin, H. / Brennan, R.G.
History
DepositionOct 4, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0May 6, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 8, 2017Group: Structure summary
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Nov 3, 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 1.6Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: PURINE REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3423
Polymers43,2082
Non-polymers1341
Water1,06359
1
B: DNA (5'-D(*TP*AP*CP*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*CP*GP*T )-3')
A: 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: PURINE REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6846
Polymers86,4164
Non-polymers2682
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)175.650, 94.680, 81.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE COMPLEX LIES ON A CRYSTALLOGRAPHIC TWO-FOLD AXIS, AND ONLY ONE MONOMER-DNA HALF-SITE CONSTITUTES THE ASYMMETRIC UNIT. THE COORDINATES COMPRISE ONE REPRESSOR MONOMER AND ONE DNA STRAND FOR THE ENTIRE SITE. THE FULL COMPLEX CAN BE CONSTRUCTED BY GENERATING THE SECOND HALF USING THE CRYSTALLOGRAPHIC SYMMETRY OPERATION (X, -Y, -Z).

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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: isolated from a genetically manipulated source
Source: (synth.) synthetic construct (others)
#2: Protein PURINE REPRESSOR


Mass: 38005.480 Da / Num. of mol.: 1 / Mutation: R190A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0ACP7
#3: Chemical ChemComp-6MP / 6-METHYLPURINE


Mass: 134.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE HYDROGEN BONDS FROM ARG 190 TO THE O6 EXOCYCLIC ATOM IS WHAT DETERMINES PURR'S SPECIFICITY FOR ...THE HYDROGEN BONDS FROM ARG 190 TO THE O6 EXOCYCLIC ATOM IS WHAT DETERMINES PURR'S SPECIFICITY FOR COREPRESSORS HYPOXANTHINE AND GUANINE AND ALLOWS IT TO DISCRIMINATE AGAINST ADENINE. MUTATING ARG 190 TO ALA RESULTS IN A PURR PROTEIN WHICH CAN BIND ADENINE IN ADDITION TO HYPOXANTHINE AND GUANINE.

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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: 3.94 Å3/Da / Density % sol: 68.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: pH 7.40, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA-K PHOSPHATE11
3DTT11
4NA CACODYLATE11
5PRECIPITATING SOLUTION11
6WATER12
7PEG 400012
8AMMONIUM SULFATE12
9COBALT HEXAMINE12
10AMMONIUM 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

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.9 Å / Num. obs: 14911 / % possible obs: 99 % / Redundancy: 3.43 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.7

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Processing

Software
NameClassification
TNTrefinement
SDMSdata reduction
SDMSdata scaling
RefinementResolution: 2.9→10 Å / Isotropic thermal model: ISOTROPIC / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.166 --
obs-14911 99 %
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2651 345 10 59 3065
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01630971.9
X-RAY DIFFRACTIONt_angle_deg1.75642432.2
X-RAY DIFFRACTIONt_dihedral_angle_d20.5117540
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle63.31151
X-RAY DIFFRACTIONt_trig_c_planes0.012673.4
X-RAY DIFFRACTIONt_gen_planes0.014094
X-RAY DIFFRACTIONt_it5.09827054.9
X-RAY DIFFRACTIONt_nbd0.06019
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 10 Å / Num. reflection all: 18818 / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_bond_d1.9
X-RAY DIFFRACTIONt_angle_deg2.2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg020.51
X-RAY DIFFRACTIONt_planar_d3.40.012
X-RAY DIFFRACTIONt_plane_restr40.01

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