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- PDB-1par: DNA RECOGNITION BY BETA-SHEETS IN THE ARC REPRESSOR-OPERATOR CRYS... -

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Basic information

Entry
Database: PDB / ID: 1par
TitleDNA RECOGNITION BY BETA-SHEETS IN THE ARC REPRESSOR-OPERATOR CRYSTAL STRUCTURE
Components
  • DNA (5'-D(*AP*AP*TP*GP*AP*TP*AP*GP*AP*AP*GP*CP*AP*CP*TP*CP*T P*AP*CP*TP*AP*T)- 3')
  • DNA (5'-D(*TP*AP*TP*AP*GP*TP*AP*GP*AP*GP*TP*GP*CP*TP*TP*CP*T P*AP*TP*CP*AP*T)- 3')
  • PROTEIN (ARC REPRESSOR)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Arc-like DNA binding domain / Arc-like DNA binding domain / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional repressor arc
Similarity search - Component
Biological speciesEnterobacteria phage P22 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsRaumann, B.E. / Rould, M.A. / Pabo, C.O. / Sauer, R.T.
CitationJournal: Nature / Year: 1994
Title: DNA recognition by beta-sheets in the Arc repressor-operator crystal structure.
Authors: Raumann, B.E. / Rould, M.A. / Pabo, C.O. / Sauer, R.T.
History
DepositionMar 22, 1994Deposition site: BNL / Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: DNA (5'-D(*TP*AP*TP*AP*GP*TP*AP*GP*AP*GP*TP*GP*CP*TP*TP*CP*T P*AP*TP*CP*AP*T)- 3')
F: DNA (5'-D(*AP*AP*TP*GP*AP*TP*AP*GP*AP*AP*GP*CP*AP*CP*TP*CP*T P*AP*CP*TP*AP*T)- 3')
A: PROTEIN (ARC REPRESSOR)
B: PROTEIN (ARC REPRESSOR)
C: PROTEIN (ARC REPRESSOR)
D: PROTEIN (ARC REPRESSOR)


Theoretical massNumber of molelcules
Total (without water)38,4536
Polymers38,4536
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.670, 56.730, 53.800
Angle α, β, γ (deg.)90.00, 106.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.5118, 0.1127, -0.8517), (0.1307, -0.9696, -0.2068), (-0.8491, -0.2172, 0.4815)63.4547, -8.0355, 35.2145
2given(0.5356, 0.0395, -0.8435), (0.0426, -0.9989, -0.0198), (-0.8434, -0.0253, -0.5367)58.0827, -4.3397, 105.3471
3given(0.0146, 0.1199, -0.9927), (0.1004, -0.9879, -0.1179), (-0.9948, -0.098, -0.0264)70.372, -5.9028, 71.2235
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN A WHEN APPLIED TO CHAIN B (DIMER SYMMETRY AXIS). THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN C WHEN APPLIED TO CHAIN D (DIMER SYMMETRY AXIS). THE TRANSFORMATION PRESENTED ON *MTRIX 3* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS A AND B WHEN APPLIED TO CHAINS C AND D, RESPECTIVELY. THIS THIRD TRANSFORMATION RELATES DIMER CD AND THE RIGHT OPERATOR HALF-SITE TO DIMER AB AND THE LEFT OPERATOR HALF-SITE. (TETRAMER SYMMETRY AXIS).

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Components

#1: DNA chain DNA (5'-D(*TP*AP*TP*AP*GP*TP*AP*GP*AP*GP*TP*GP*CP*TP*TP*CP*T P*AP*TP*CP*AP*T)- 3')


Mass: 6756.387 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*AP*TP*GP*AP*TP*AP*GP*AP*AP*GP*CP*AP*CP*TP*CP*T P*AP*CP*TP*AP*T)- 3')


Mass: 6743.404 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein
PROTEIN (ARC REPRESSOR)


Mass: 6238.272 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / References: UniProt: P03050
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.4 / Details: pH 7.40, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2BIS-TRIS-PROPANE11
3NA AZIDE11
4WATER12
5PEG 40012
6MGCL212
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.58 mMArc tetramer1drop
20.93 mMDNA duplex1drop
330 mMBis-Tris-propane-Cl1droppH7.4
41 mM1dropNaN3
515 %PEG4001reservoir
6100 mM1reservoirMgCl2

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Data collection

DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.6 Å / Num. all: 161619 / Num. obs: 11253
Reflection
*PLUS
Highest resolution: 2.6 Å / % possible obs: 95 % / Num. measured all: 161619 / Rmerge(I) obs: 0.114

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.6→21 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.225 11253 95 %
Refinement stepCycle: LAST / Resolution: 2.6→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1712 896 0 45 2653
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.51
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 / Lowest resolution: 21 Å / Rfactor obs: 0.225 / Rfactor Rwork: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS

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