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- PDB-4ft8: E. coli Catabolite Activator Protein with Cobalt and Sulfate Ligands -

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Basic information

Entry
Database: PDB / ID: 4ft8
TitleE. coli Catabolite Activator Protein with Cobalt and Sulfate Ligands
ComponentsCatabolite gene activator
KeywordsTRANSCRIPTION ACTIVATOR / winged helix-turn-helix / DNA binding protein / Cobalt binding / Sulfate binding
Function / homology
Function and homology information


carbon catabolite repression of transcription / DNA binding, bending / minor groove of adenine-thymine-rich DNA binding / cAMP binding / protein-DNA complex / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription ...carbon catabolite repression of transcription / DNA binding, bending / minor groove of adenine-thymine-rich DNA binding / cAMP binding / protein-DNA complex / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
: / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site ...: / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / 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 / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / 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-binding transcriptional dual regulator CRP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.966 Å
AuthorsRao, R. / Lawson, C.L.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Structure of catabolite activator protein with cobalt(II) and sulfate.
Authors: Rao, R.R. / Lawson, C.L.
History
DepositionJun 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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
A: Catabolite gene activator
B: Catabolite gene activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,10819
Polymers47,0822
Non-polymers2,02517
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-201 kcal/mol
Surface area19520 Å2
MethodPISA
2
B: Catabolite gene activator
hetero molecules

A: Catabolite gene activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,10819
Polymers47,0822
Non-polymers2,02517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area4890 Å2
ΔGint-204 kcal/mol
Surface area21690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.143, 108.452, 44.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-488-

HOH

21A-543-

HOH

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Components

#1: Protein Catabolite gene activator / cAMP receptor protein / cAMP regulatory protein


Mass: 23541.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b3357, cap, crp, csm, JW5702 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ACJ8
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: A CAP-DNA complex was screened by hanging-drop vapor diffusion with Hampton Research Crystal Screens and pregreased VDX plates. Optimization of Crystal Screen 2 condition #25 yielded ruby- ...Details: A CAP-DNA complex was screened by hanging-drop vapor diffusion with Hampton Research Crystal Screens and pregreased VDX plates. Optimization of Crystal Screen 2 condition #25 yielded ruby-red colored crystals appearing within 3 days at 20 C in 0.01 M CoCl2.6H2O, 0.1 M MES monohydrate pH 6.5 and 2.5 M (NH4)2SO4. The crystallization process yielded crystals containing only CAP protein without DNA, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 16, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. all: 35645 / Num. obs: 35645 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.088 / Χ2: 1.949 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.96-2.034.20.77832801.787190.5
2.03-2.1150.57534882.795196.5
2.11-2.215.30.41535291.597197
2.21-2.325.30.32534921.588197.2
2.32-2.475.30.24335421.507197.5
2.47-2.665.30.1835431.434197.8
2.66-2.935.20.12336001.435198.3
2.93-3.355.20.07236251.775198.3
3.35-4.225.10.04436731.721198.8
4.22-504.90.04138733.878198.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: search 1: 1ZRC CAP N-terminal domain dimer; searches 2,3: 1ZRC CAP individual C-terminal domain

1zrc

1zrc


Resolution: 1.966→40.781 Å / Occupancy max: 1 / Occupancy min: 0.24 / SU ML: 0.15 / σ(F): 1.34 / Phase error: 24.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1774 4.98 %random
Rwork0.1959 ---
obs0.1977 35596 97.3 %-
all-35645 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.415 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 107.66 Å2 / Biso mean: 35.2859 Å2 / Biso min: 9.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.6641 Å20 Å20 Å2
2---0.4729 Å2-0 Å2
3----0.1912 Å2
Refinement stepCycle: LAST / Resolution: 1.966→40.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 111 409 3683
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_deg1
X-RAY DIFFRACTIONf_dihedral_angle_d16.888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.9663-2.01940.32161130.2865X-RAY DIFFRACTION257992
4.6212-40.78950.20491410.195X-RAY DIFFRACTION297798

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