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- PDB-1u9p: Permuted single-chain Arc -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1u9p
TitlePermuted single-chain Arc
ComponentspArc
KeywordsUNKNOWN FUNCTION / Arc / pArc
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
Transcriptional repressor arc
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsTabtiang, R.K. / Cezairliyan, B.O. / Grant, R.A. / Cochrane, J.C. / Sauer, R.T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Consolidating critical binding determinants by noncyclic rearrangement of protein secondary structure
Authors: Tabtiang, R.K. / Cezairliyan, B.O. / Grant, R.A. / Cochrane, J.C. / Sauer, R.T.
History
DepositionAug 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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

Downloads & links

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Assembly

Deposited unit
A: pArc


Theoretical massNumber of molelcules
Total (without water)13,7611
Polymers13,7611
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.181, 62.916, 30.380
Angle α, β, γ (deg.)90.00, 102.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein pArc


Mass: 13760.583 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P03050*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, sodium fluoride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 8-BM10.979
ROTATING ANODERIGAKU RU20021.541
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 16, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.5411
ReflectionResolution: 1.9→20 Å / Num. all: 8500 / Num. obs: 8500 / % possible obs: 95 % / Rsym value: 0.067 / Net I/σ(I): 11.5
Reflection shellHighest resolution: 1.9 Å / Rsym value: 0.195 / % possible all: 75.8

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.297 833 random
Rwork0.249 --
all0.253 7859 -
obs0.253 7859 -
Solvent computationBsol: 56.816 Å2 / ksol: 0.396375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.594 Å20 Å2-3.276 Å2
2--0.512 Å20 Å2
3---5.082 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms782 0 0 53 835
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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