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- PDB-1wet: STRUCTURE OF THE PURR-GUANINE-PURF OPERATOR COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1wet
TitleSTRUCTURE OF THE PURR-GUANINE-PURF OPERATOR COMPLEX
Components
  • DNA (5'-D(*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*TP*TP*TP*TP*CP*GP*T )-3')
  • PROTEIN (PURINE REPRESSOR)
KeywordsTRANSCRIPTION/DNA / DNA-BINDING REGULATORY PROTEIN / REPRESSOR / 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 / 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
GUANINE / DNA / DNA (> 10) / HTH-type transcriptional repressor PurR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsSchumacher, M.A. / Glasfeld, A. / Zalkin, H. / Brennan, R.G.
Citation
Journal: J.Biol.Chem. / Year: 1997
Title: The X-ray structure of the PurR-guanine-purF operator complex reveals the contributions of complementary electrostatic surfaces and a water-mediated hydrogen bond to corepressor specificity and binding affinity.
Authors: Schumacher, M.A. / Glasfeld, A. / 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
DepositionApr 27, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Nov 21, 1997Provider: 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 1.4Feb 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
B: DNA (5'-D(*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*TP*TP*TP*TP*CP*GP*T )-3')
A: PROTEIN (PURINE REPRESSOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4533
Polymers43,3022
Non-polymers1511
Water82946
1
B: DNA (5'-D(*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*TP*TP*TP*TP*CP*GP*T )-3')
A: PROTEIN (PURINE REPRESSOR)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)86,9066
Polymers86,6044
Non-polymers3022
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)175.990, 95.080, 81.510
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(*AP*AP*CP*GP*AP*AP*AP*AP*CP*GP*TP*TP*TP*TP*CP*GP*T )-3')


Mass: 5210.410 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein PROTEIN (PURINE REPRESSOR)


Mass: 38091.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / 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.: 46 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.76 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5 / Details: pH 7.50, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 400011
3NH4 SULFATE11
4[CO(NH3)6]CL311
5NH4 PHOSPHATE11
6WATER12
7PEG 400012
8NH4 SULFATE12
9[CO(NH3)6]CL312
10NH4 PHOSPHATE12
Crystal grow
*PLUS
pH: 7.5 / 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 mMDTT1drop
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

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorDetector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / % possible obs: 87 % / Redundancy: 3 % / Rmerge(I) obs: 0.0629 / Net I/σ(I): 7.4
Reflection shellResolution: 2.5→2.7 Å / Mean I/σ(I) obs: 1.4 / % possible all: 78
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / % possible obs: 87 %
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.7 Å / % possible obs: 78 %

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Processing

SoftwareName: TNT / Classification: refinement
RefinementHighest resolution: 2.6 Å / σ(F): 1 /
RfactorNum. reflection
obs0.176 21013
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 346 11 46 3055
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_deg2.26
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
Refinement
*PLUS
Highest resolution: 2.6 Å / σ(F): 1 / Rfactor Rwork: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS

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