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- PDB-1lb2: Structure of the E. coli alpha C-terminal domain of RNA polymeras... -

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Basic information

Entry
Database: PDB / ID: 1lb2
TitleStructure of the E. coli alpha C-terminal domain of RNA polymerase in complex with CAP and DNA
Components
  • 5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*AP*G)-3'
  • 5'-D(*CP*TP*TP*TP*TP*TP*TP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3'
  • CATABOLITE GENE ACTIVATOR PROTEINCAMP receptor protein
  • DNA-directed RNA polymerase alpha chain
KeywordsGENE REGULATION/DNA / PROTEIN-DNA COMPLEX / GENE-REGULATORY / GENE REGULATION-DNA COMPLEX
Function / homology
Function and homology information


carbon catabolite repression of transcription / DNA binding, bending / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / minor groove of adenine-thymine-rich DNA binding / bacterial-type flagellum-dependent cell motility / nitrate assimilation ...carbon catabolite repression of transcription / DNA binding, bending / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / minor groove of adenine-thymine-rich DNA binding / bacterial-type flagellum-dependent cell motility / nitrate assimilation / cAMP binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / cell motility / protein-DNA complex / DNA-templated transcription initiation / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / intracellular iron ion homeostasis / sequence-specific DNA binding / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain ...Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / 5' to 3' exonuclease, C-terminal subdomain / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / DNA polymerase; domain 1 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / DNA / DNA (> 10) / DNA-directed RNA polymerase subunit alpha / DNA-binding transcriptional dual regulator CRP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, FOURIER SYNTHESIS / Resolution: 3.1 Å
AuthorsBenoff, B. / Yang, H. / Lawson, C.L. / Parkinson, G. / Liu, J. / Blatter, E. / Ebright, Y.W. / Berman, H.M. / Ebright, R.H.
CitationJournal: Science / Year: 2002
Title: Structural basis of transcription activation: the CAP-alpha CTD-DNA complex.
Authors: Benoff, B. / Yang, H. / Lawson, C.L. / Parkinson, G. / Liu, J. / Blatter, E. / Ebright, Y.W. / Berman, H.M. / Ebright, R.H.
History
DepositionApr 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
K: 5'-D(*CP*TP*TP*TP*TP*TP*TP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3'
J: 5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*AP*G)-3'
A: CATABOLITE GENE ACTIVATOR PROTEIN
B: DNA-directed RNA polymerase alpha chain
E: DNA-directed RNA polymerase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0996
Polymers55,7705
Non-polymers3291
Water57632
1
K: 5'-D(*CP*TP*TP*TP*TP*TP*TP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3'
J: 5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*AP*G)-3'
A: CATABOLITE GENE ACTIVATOR PROTEIN
B: DNA-directed RNA polymerase alpha chain
E: DNA-directed RNA polymerase alpha chain
hetero molecules

K: 5'-D(*CP*TP*TP*TP*TP*TP*TP*CP*CP*TP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3'
J: 5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*AP*G)-3'
A: CATABOLITE GENE ACTIVATOR PROTEIN
B: DNA-directed RNA polymerase alpha chain
E: DNA-directed RNA polymerase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,19812
Polymers111,53910
Non-polymers6582
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Unit cell
Length a, b, c (Å)175.970, 175.970, 158.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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DNA chain , 2 types, 2 molecules KJ

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


Mass: 6088.962 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*AP*GP*GP*AP*AP*AP*AP*AP*AP*G)-3'


Mass: 7409.844 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 2 types, 3 molecules ABE

#3: Protein CATABOLITE GENE ACTIVATOR PROTEIN / CAMP receptor protein / CAP / cAMP receptor protein / cAMP-regulatory protein


Mass: 23541.242 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: P0ACJ8
#4: Protein DNA-directed RNA polymerase alpha chain / Transcriptase alpha chain / RNA polymerase alpha subunit


Mass: 9364.795 Da / Num. of mol.: 2 / Fragment: alpha CTD, alpha Carboxy terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase

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Non-polymers , 2 types, 33 molecules

#5: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 6 Å3/Da / Density % sol: 78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: NaCl, NaAcetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaClSodium chloride11
2Na(C2H3O2)11
3NaClSodium chloride12
4Na(C2H3O2)12
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1-0.2 mMCAP1drop
20.2-0.4 mMalpha-CTD1drop
30.1-0.3 mMDNA1drop
40.8 mMcAMP1drop
650 mMsodium acetate1reservoirpH4.5
7250 mM1reservoirNaCl
5reservoir1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jul 6, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.1→20 Å / Num. all: 23331 / Num. obs: 23331 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.3 % / Biso Wilson estimate: 81.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.7
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 1.5 / % possible all: 38.5
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 88 % / Num. measured all: 332877

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, FOURIER SYNTHESIS
Starting model: 2CGP

2cgp


Resolution: 3.1→20 Å / Rfactor Rfree error: 0.005 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2304 9.9 %random
Rwork0.211 ---
all-23331 --
obs-23331 87.9 %-
Solvent computationSolvent model: flat model / Bsol: 47.7314 Å2 / ksol: 0.272486 e/Å3
Displacement parametersBiso mean: 104.2 Å2
Baniso -1Baniso -2Baniso -3
1-16.45 Å217.05 Å20 Å2
2--16.45 Å20 Å2
3----32.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.83 Å0.79 Å
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2663 896 22 32 3613
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d21.2
X-RAY DIFFRACTIONx_improper_angle_d1.03
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.475 182 9.6 %
Rwork0.448 1705 -
obs--43.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_rep.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna_rep.top
X-RAY DIFFRACTION3cmp.paramcmp.top
X-RAY DIFFRACTION4water_rep.paramwater_rep.top
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.03

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