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

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Basic information

Entry
Database: PDB / ID: 2puf
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')
  • PROTEIN (PURINE REPRESSOR)
KeywordsTRANSCRIPTION/DNA / COMPLEX (DNA-BINDING PROTEIN-DNA) / DNA-BINDING REGULATORY PROTEIN / EXTENDED COREPRESSOR SPECIFICITY / 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
GUANINE / DNA / DNA (> 10) / HTH-type transcriptional repressor PurR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsLu, F. / Schumacher, M.A. / Arvidson, D.N. / Haldimann, A. / Wanner, B.L. / Zalkin, H. / Brennan, R.G.
Citation
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.
#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
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 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Nov 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 1.5Feb 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: PROTEIN (PURINE REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4163
Polymers43,2652
Non-polymers1511
Water63135
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)86,8326
Polymers86,5304
Non-polymers3022
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)175.920, 95.050, 81.590
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: obtained synthetically
#2: Protein PROTEIN (PURINE REPRESSOR)


Mass: 38062.531 Da / Num. of mol.: 1 / Mutation: R190Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURR / Plasmid: PDNA100 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0ACP7
#3: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE HYDROGEN BONDS FROM ARG 190 DETERMINE SPECIFICITY FOR THE O6 EXOCYCLIC ATOM OF THE NATURAL ...THE HYDROGEN BONDS FROM ARG 190 DETERMINE SPECIFICITY FOR THE O6 EXOCYCLIC ATOM OF THE NATURAL COREPRESSORS HYPOXANTHINE AND GUANINE AND PREVENT ADENINE BINDING. SUBSTITUTING ARG 190 WITH GLN YIELDS A MUTANT PURR WITH EXTENDED COREPRESSOR SPECIFICITY WHICH BINDS 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: 68.79 %
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
7AMMONIUM SULFATE12
8COBALT HEXAMINE12
9AMMONIUM PHOSPHATE12
10PEG 400012
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: 3 Å / Num. obs: 13317 / % possible obs: 96 % / Redundancy: 3.75 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 3.6
Reflection
*PLUS
Highest resolution: 3 Å / % possible obs: 96 % / Num. measured all: 49911

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Processing

Software
NameClassification
TNTrefinement
ADSCdata collection
RefinementResolution: 3→10 Å / Isotropic thermal model: ISOTROPIC / σ(F): 1 / Stereochemistry target values: ENGH AND HUBER /
RfactorNum. reflection% reflection
obs0.222 13317 96 %
Solvent computationSolvent model: TNT / Bsol: 150 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2650 345 11 35 3041
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00931023.1
X-RAY DIFFRACTIONt_angle_deg0.85442535.5
X-RAY DIFFRACTIONt_dihedral_angle_d21.917540
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.015683
X-RAY DIFFRACTIONt_gen_planes0.0084135
X-RAY DIFFRACTIONt_it2.5827042.5
X-RAY DIFFRACTIONt_nbd0.04333617
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / σ(F): 1 / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_bond_d3.1
X-RAY DIFFRACTIONt_angle_deg5.5
X-RAY DIFFRACTIONt_dihedral_angle_d021.9
X-RAY DIFFRACTIONt_planar_d30.015
X-RAY DIFFRACTIONt_plane_restr50.008

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