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- PDB-1ny6: Crystal structure of sigm54 activator (AAA+ ATPase) in the active... -

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Basic information

Entry
Database: PDB / ID: 1ny6
TitleCrystal structure of sigm54 activator (AAA+ ATPase) in the active state
Componentstranscriptional regulator (NtrC family)
KeywordsTRANSCRIPTION / AAA+ ATPase / sigma54 activator / bacterial transcription / heptamer
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Helicase, Ruva Protein; domain 3 - #60 ...Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Helicase, Ruva Protein; domain 3 - #60 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Helicase, Ruva Protein; domain 3 / Homeobox-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Transcriptional regulator (NtrC family)
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLee, S.Y. / de la Torre, A. / Kustu, S. / Nixon, B.T. / Wemmer, D.E.
CitationJournal: Genes Dev. / Year: 2003
Title: Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains
Authors: Lee, S.Y. / de la Torre, A. / Yan, D. / Kustu, S. / Nixon, B.T. / Wemmer, D.E.
History
DepositionFeb 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: transcriptional regulator (NtrC family)
B: transcriptional regulator (NtrC family)
C: transcriptional regulator (NtrC family)
D: transcriptional regulator (NtrC family)
E: transcriptional regulator (NtrC family)
F: transcriptional regulator (NtrC family)
G: transcriptional regulator (NtrC family)
H: transcriptional regulator (NtrC family)
I: transcriptional regulator (NtrC family)
J: transcriptional regulator (NtrC family)
K: transcriptional regulator (NtrC family)
L: transcriptional regulator (NtrC family)
M: transcriptional regulator (NtrC family)
N: transcriptional regulator (NtrC family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)434,63928
Polymers428,65814
Non-polymers5,98114
Water0
1
A: transcriptional regulator (NtrC family)
B: transcriptional regulator (NtrC family)
C: transcriptional regulator (NtrC family)
D: transcriptional regulator (NtrC family)
E: transcriptional regulator (NtrC family)
F: transcriptional regulator (NtrC family)
G: transcriptional regulator (NtrC family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,32014
Polymers214,3297
Non-polymers2,9907
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: transcriptional regulator (NtrC family)
I: transcriptional regulator (NtrC family)
J: transcriptional regulator (NtrC family)
K: transcriptional regulator (NtrC family)
L: transcriptional regulator (NtrC family)
M: transcriptional regulator (NtrC family)
N: transcriptional regulator (NtrC family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,32014
Polymers214,3297
Non-polymers2,9907
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.788, 108.265, 110.020
Angle α, β, γ (deg.)70.25, 85.90, 73.27
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a heptamer that forms a ring-like structure in the assymetric unit (there are 14 molecules in the assymetric unit)

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Components

#1: Protein
transcriptional regulator (NtrC family)


Mass: 30618.445 Da / Num. of mol.: 14 / Fragment: residues 122-387
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: NtrC1 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: O67198
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.92 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: diammonium tartrate, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
250 mMdiammonium tartrate1reservoirpH6.5
38 %(v/v)PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 17, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→62.02 Å / Num. obs: 86929 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 103 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 7.8
Reflection shellResolution: 3.1→3.27 Å / % possible all: 97.1
Reflection shell
*PLUS
% possible obs: 97.1 % / Rmerge(I) obs: 0.421

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→19.98 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.329 7844 10 %RANDOM
Rwork0.266 ---
all0.272 ---
obs0.266 78375 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.221601 e/Å3
Displacement parametersBiso mean: 103.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.64 Å2-26.61 Å2-8.84 Å2
2---0.09 Å2-16.43 Å2
3----5.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.69 Å0.56 Å
Luzzati d res low-5 Å
Luzzati sigma a0.94 Å0.88 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27663 0 378 0 28041
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.473 1286 9.9 %
Rwork0.462 11738 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ADP_XPLOR2.PARADP_XPLOR2.TOP
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11

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