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- PDB-1vpw: STRUCTURE OF THE PURR MUTANT, L54M, BOUND TO HYPOXANTHINE AND PUR... -

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Basic information

Entry
Database: PDB / ID: 1vpw
TitleSTRUCTURE OF THE PURR MUTANT, L54M, BOUND TO HYPOXANTHINE AND PURF OPERATOR DNA
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 / MINOR GROOVE BENDING / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsArvidson, D.N. / Lu, F. / Faber, C. / Zalkin, H. / Brennan, R.G.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: The structure of PurR mutant L54M shows an alternative route to DNA kinking.
Authors: Arvidson, D.N. / Lu, F. / Faber, C. / Zalkin, H. / Brennan, R.G.
History
DepositionFeb 27, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 15, 2017Group: Source and taxonomy / Structure summary
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 14, 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)43,4483
Polymers43,3122
Non-polymers1361
Water90150
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)86,8966
Polymers86,6244
Non-polymers2722
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)175.890, 94.930, 81.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
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') / PURF OPERATOR


Mass: 5202.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein PURINE REPRESSOR


Mass: 38109.633 Da / Num. of mol.: 1 / Mutation: L54M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: 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.: 50 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE LEUCINE 54 LEVERS INTERDIGITATE FROM THE MINOR GROOVE SIDE BETWEEN THE CENTRAL C.G:G.C BASE ...THE LEUCINE 54 LEVERS INTERDIGITATE FROM THE MINOR GROOVE SIDE BETWEEN THE CENTRAL C.G:G.C BASE PAIR STEP OF PURF OPERATOR DNA. THE OPERATOR DNA IS THUS KINKED BY 50 DEGREES. SUBSTITUTING LEU 54 WITH MET YIELDS A MUTANT PURR THAT BINDS AND BENDS DNA SIMILARLY TO WILD TYPE. HOWEVER, THE ROUTES OF THE SIDE CHAINS AND THEIR CONTACTS TO THE C-G:G-C BASE PAIR STEP DIFFER.

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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: 3.95 Å3/Da / Density % sol: 68.83 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Schumacher, M.A., (1994) J.Mol.Biol, 242, 302.
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 Mammonium sulfate1drop
850 mMcobalt hexammine1drop
90.1 Mammonium phosphate1drop
1025 %PEG40001reservoir
110.4 Mammonium sulfate1reservoir
1250 mMcobalt hexammine1reservoir
130.1 Mammonium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.7 Å / Num. obs: 18486 / % possible obs: 98 % / Net I/σ(I): 8.8
Reflection shellResolution: 2.7→2.9 Å / % possible all: 79
Reflection
*PLUS
Highest resolution: 2.7 Å / % possible obs: 98 % / Num. measured all: 71433 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.9 Å / % possible obs: 79 % / Mean I/σ(I) obs: 1.7

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.7→10 Å / Isotropic thermal model: TNT / σ(F): 1.3 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
Rwork0.174 --
obs-18486 98 %
Solvent computationBsol: 150 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 345 10 50 3057
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01331032.5
X-RAY DIFFRACTIONt_angle_deg1.2842524
X-RAY DIFFRACTIONt_dihedral_angle_d20.9317570
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.017673
X-RAY DIFFRACTIONt_gen_planes0.014145
X-RAY DIFFRACTIONt_it5.82727062.5
X-RAY DIFFRACTIONt_nbd0.06531215
LS refinement shellResolution: 2.7→2.9 Å / % reflection obs: 79 %
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 10 Å / σ(F): 1.3 / Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.930
X-RAY DIFFRACTIONt_plane_restr0.015

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