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- PDB-2r1j: Crystal Structure of the P22 c2 Repressor protein in complex with... -

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Basic information

Entry
Database: PDB / ID: 2r1j
TitleCrystal Structure of the P22 c2 Repressor protein in complex with the synthetic operator 9T
Components
  • 5'-D(*DCP*DAP*DTP*DTP*DTP*DAP*DAP*DGP*DAP*DTP*DAP*DTP*DCP*DTP*DTP*DAP*DAP*DAP*DTP*DA)-3'
  • 5'-D(*DTP*DAP*DTP*DTP*DTP*DAP*DAP*DGP*DAP*DTP*DAP*DTP*DCP*DTP*DTP*DAP*DAP*DAP*DTP*DG)-3'
  • Repressor protein C2
KeywordsTRANSCRIPTION/DNA / Protein-DNA complex / Helix-turn-helix / DNA-binding / Repressor / Transcription / Transcription regulation / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


: / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain ...: / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Repressor protein C2
Similarity search - Component
Biological speciesEnterobacteria phage P22 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 Å
AuthorsWilliams, L.D. / Koudelka, G.B. / Watkins, D. / Hsiao, C. / Woods, K.
CitationJournal: Biochemistry / Year: 2008
Title: P22 c2 repressor-operator complex: mechanisms of direct and indirect readout
Authors: Watkins, D. / Hsiao, C. / Woods, K.K. / Koudelka, G.B. / Williams, L.D.
History
DepositionAug 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 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
B: 5'-D(*DCP*DAP*DTP*DTP*DTP*DAP*DAP*DGP*DAP*DTP*DAP*DTP*DCP*DTP*DTP*DAP*DAP*DAP*DTP*DA)-3'
A: 5'-D(*DTP*DAP*DTP*DTP*DTP*DAP*DAP*DGP*DAP*DTP*DAP*DTP*DCP*DTP*DTP*DAP*DAP*DAP*DTP*DG)-3'
L: Repressor protein C2
R: Repressor protein C2


Theoretical massNumber of molelcules
Total (without water)27,5134
Polymers27,5134
Non-polymers00
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-39.4 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.105, 64.105, 101.685
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: DNA chain 5'-D(*DCP*DAP*DTP*DTP*DTP*DAP*DAP*DGP*DAP*DTP*DAP*DTP*DCP*DTP*DTP*DAP*DAP*DAP*DTP*DA)-3'


Mass: 6115.016 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*DTP*DAP*DTP*DTP*DTP*DAP*DAP*DGP*DAP*DTP*DAP*DTP*DCP*DTP*DTP*DAP*DAP*DAP*DTP*DG)-3'


Mass: 6146.026 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Repressor protein C2


Mass: 7625.878 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / Gene: c2 / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P69202
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: The initial crystallization solution contained 0.42 mM P22R NTD, 0.42 mM duplex d(5 TATTTAAGATATCTTAAATG3 ) -d(5 CATTTAAGATATCTTAAATA3 ), 45 mM Tris.HCl (pH 7.8), 19 mM NaCl, 1.9 mM ...Details: The initial crystallization solution contained 0.42 mM P22R NTD, 0.42 mM duplex d(5 TATTTAAGATATCTTAAATG3 ) -d(5 CATTTAAGATATCTTAAATA3 ), 45 mM Tris.HCl (pH 7.8), 19 mM NaCl, 1.9 mM glycerol, 11% PEG 400, 4.5 mM LiCl, 2.3mM MgCl2 and 0.91% MPD in a volume of 5.3 ul. The crystallization solution was equilibrated against a reservoir of 100 mM Tris.HCl (pH 7.8), 25% PEG 400, 10 mM LiCl, 5 mM MgCl2 and 2% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris.HCl11
2NaCl11
3glycerol11
4PEG 40011
5LiCl11
6MgCl211
7MPD11
8Tris.HCl12
9PEG 40012
10LiCl12
11MgCl212
12MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99997 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.999971
211
ReflectionResolution: 1.53→35 Å / Num. all: 60878 / Num. obs: 60878 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rsym value: 0.069 / Net I/σ(I): 47.1
Reflection shellResolution: 1.53→1.57 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 2.12 / Num. unique all: 4319 / Rsym value: 0.659 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRCor.coef. Fo:Fc: 0.847 / Packing: 0.311
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation3 Å15 Ågeneral98.4 0

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→35 Å / FOM work R set: 0.825 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.225 6068 9.8 %
Rwork0.204 --
obs-59833 96.9 %
Solvent computationBsol: 58.05 Å2
Displacement parametersBiso mean: 31.053 Å2
Refinement stepCycle: LAST / Resolution: 1.53→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 814 0 331 2175
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.334
X-RAY DIFFRACTIONc_mcbond_it1.2781.5
X-RAY DIFFRACTIONc_scbond_it1.9832
X-RAY DIFFRACTIONc_mcangle_it2.0062
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 1.53→1.58 Å
RfactorNum. reflection% reflection
Rfree0.34 535 -
Rwork0.356 --
obs-5325 86.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep_tinoush.paramdna-rna_tinoush.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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