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- PDB-1d5y: CRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMP... -

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Basic information

Entry
Database: PDB / ID: 1d5y
TitleCRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMPLEX WITH DNA
Components
  • DNA (5'-D(*AP*CP*TP*TP*TP*GP*AP*CP*AP*TP*TP*CP*AP*GP*TP*GP*CP*TP*GP*TP*C)-3')
  • DNA (5'-D(*TP*GP*AP*CP*AP*GP*CP*AP*CP*TP*GP*AP*AP*TP*GP*TP*CP*AP*AP*AP*G)-3')
  • ROB TRANSCRIPTION FACTOR
Keywordstranscription/DNA / Protein-DNA complex / Rob Transcription factor / DNA / transcription-DNA COMPLEX
Function / homology
Function and homology information


bacterial-type RNA polymerase holo enzyme binding / sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / cytosol
Similarity search - Function
: / Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / GyrI-like small molecule binding domain / GyrI-like small molecule binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / Transcription regulator HTH, AraC- type / Regulatory factor, effector binding domain superfamily / HTH domain AraC-type, conserved site ...: / Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / GyrI-like small molecule binding domain / GyrI-like small molecule binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / Transcription regulator HTH, AraC- type / Regulatory factor, effector binding domain superfamily / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Right origin-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsKwon, H.J. / Bennik, M.H.J. / Demple, B. / Ellenberger, T.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA.
Authors: Kwon, H.J. / Bennik, M.H. / Demple, B. / Ellenberger, T.
History
DepositionOct 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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
M: DNA (5'-D(*TP*GP*AP*CP*AP*GP*CP*AP*CP*TP*GP*AP*AP*TP*GP*TP*CP*AP*AP*AP*G)-3')
N: DNA (5'-D(*AP*CP*TP*TP*TP*GP*AP*CP*AP*TP*TP*CP*AP*GP*TP*GP*CP*TP*GP*TP*C)-3')
O: DNA (5'-D(*TP*GP*AP*CP*AP*GP*CP*AP*CP*TP*GP*AP*AP*TP*GP*TP*CP*AP*AP*AP*G)-3')
P: DNA (5'-D(*AP*CP*TP*TP*TP*GP*AP*CP*AP*TP*TP*CP*AP*GP*TP*GP*CP*TP*GP*TP*C)-3')
A: ROB TRANSCRIPTION FACTOR
D: ROB TRANSCRIPTION FACTOR
C: ROB TRANSCRIPTION FACTOR
B: ROB TRANSCRIPTION FACTOR


Theoretical massNumber of molelcules
Total (without water)159,3458
Polymers159,3458
Non-polymers00
Water00
1
M: DNA (5'-D(*TP*GP*AP*CP*AP*GP*CP*AP*CP*TP*GP*AP*AP*TP*GP*TP*CP*AP*AP*AP*G)-3')
N: DNA (5'-D(*AP*CP*TP*TP*TP*GP*AP*CP*AP*TP*TP*CP*AP*GP*TP*GP*CP*TP*GP*TP*C)-3')
A: ROB TRANSCRIPTION FACTOR
B: ROB TRANSCRIPTION FACTOR


Theoretical massNumber of molelcules
Total (without water)79,6734
Polymers79,6734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
O: DNA (5'-D(*TP*GP*AP*CP*AP*GP*CP*AP*CP*TP*GP*AP*AP*TP*GP*TP*CP*AP*AP*AP*G)-3')
P: DNA (5'-D(*AP*CP*TP*TP*TP*GP*AP*CP*AP*TP*TP*CP*AP*GP*TP*GP*CP*TP*GP*TP*C)-3')
D: ROB TRANSCRIPTION FACTOR
C: ROB TRANSCRIPTION FACTOR


Theoretical massNumber of molelcules
Total (without water)79,6734
Polymers79,6734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.384, 208.012, 67.731
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: DNA chain DNA (5'-D(*TP*GP*AP*CP*AP*GP*CP*AP*CP*TP*GP*AP*AP*TP*GP*TP*CP*AP*AP*AP*G)-3')


Mass: 6480.225 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*CP*TP*TP*TP*GP*AP*CP*AP*TP*TP*CP*AP*GP*TP*GP*CP*TP*GP*TP*C)-3')


Mass: 6404.144 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein
ROB TRANSCRIPTION FACTOR / RIGHT ORIGIN-BINDING PROTEIN


Mass: 33394.137 Da / Num. of mol.: 4 / Fragment: RESIDUES 3-289, KLAAA EXTENSION AFTER RESIDUE 289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACI0

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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: 3.31 Å3/Da / Density % sol: 62.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Peg 8000, MES, MgCl2, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2MGCL211
3GLYCEROL11
4PEG 800011
5GLYCEROL12
6PEG 800012
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
2100 mMMES1reservoir
3125 mM1reservoirMgCl2
410 %(v/v)glycerol1reservoir
51 mMdithiothreitol1reservoir
61 mMspermine-HCl1reservoir
715 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9161
DetectorType: OTHER / Detector: CCD / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9161 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 54476 / Num. obs: 54476 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.426 / Num. unique all: 4992 / % possible all: 87.2
Reflection
*PLUS
Num. measured all: 306889

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.302 3812 7 %random
Rwork0.254 ---
all0.254 54222 --
obs0.254 54222 95.1 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.171 Å20 Å20 Å2
2---0.324 Å20 Å2
3---6.494 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9280 1710 0 0 10990
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_bond_d0.0075
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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