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- PDB-3dzd: Crystal structure of sigma54 activator NTRC4 in the inactive state -

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Basic information

Entry
Database: PDB / ID: 3dzd
TitleCrystal structure of sigma54 activator NTRC4 in the inactive state
ComponentsTranscriptional regulator (NtrC family)
KeywordsTRANSCRIPTION REGULATOR / Sigma43 activator / AAA+ ATPase / response regulator / transcriptional activator / ATP-binding / Nucleotide-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Sigma-54 interaction domain ATP-binding region A 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 ...Sigma-54 interaction domain ATP-binding region A 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 / Response regulator / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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 / molecular replacement / Resolution: 2.4 Å
AuthorsBatchelor, J.D. / Doucleff, M. / Lee, C.-J. / Matsubara, K. / De Carlo, S. / Heideker, J. / Lamers, M.M. / Pelton, J.G. / Wemmer, D.E.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure and regulatory mechanism of Aquifex aeolicus NtrC4: variability and evolution in bacterial transcriptional regulation.
Authors: Batchelor, J.D. / Doucleff, M. / Lee, C.J. / Matsubara, K. / De Carlo, S. / Heideker, J. / Lamers, M.H. / Pelton, J.G. / Wemmer, D.E.
History
DepositionJul 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7735
Polymers83,8962
Non-polymers8773
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-20 kcal/mol
Surface area34810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.897, 93.105, 114.163
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcriptional regulator (NtrC family)


Mass: 41948.012 Da / Num. of mol.: 2 / Fragment: UNP residues 2 to 369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_164, ntrC4 / Plasmid: PSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66551
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 298 K / pH: 4.6
Details: 5% PEG 4000, 150mM NaCl, 50mM Citric Acid, 5% Glycerol, pH 4.6, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.28237 / Wavelength: 1.28237 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2005 / Details: OPTICS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28237 Å / Relative weight: 1
ReflectionResolution: 2.4→68.52 Å / Num. all: 38157 / Num. obs: 37966 / % possible obs: 99.5 % / Observed criterion σ(F): 1.36 / Redundancy: 3.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2 / Rsym value: 0.496 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1ny5

1ny5


Resolution: 2.4→35.04 Å / Occupancy max: 1 / Occupancy min: 0.51 / SU ML: 0.4 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 1579 4.16 %
Rwork0.214 --
obs0.216 37966 99.5 %
all-38141 -
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.69 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 63.85 Å2
Baniso -1Baniso -2Baniso -3
1--1.542 Å20 Å20 Å2
2---1.028 Å2-0 Å2
3---2.57 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5898 0 55 250 6203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066062
X-RAY DIFFRACTIONf_angle_d0.9618160
X-RAY DIFFRACTIONf_dihedral_angle_d16.3982322
X-RAY DIFFRACTIONf_chiral_restr0.062912
X-RAY DIFFRACTIONf_plane_restr0.0041034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4770.3111410.2613251X-RAY DIFFRACTION100
2.477-2.5660.3231420.2453269X-RAY DIFFRACTION100
2.566-2.6690.2831420.2553271X-RAY DIFFRACTION100
2.669-2.790.3581410.2543274X-RAY DIFFRACTION100
2.79-2.9370.3071430.2553274X-RAY DIFFRACTION100
2.937-3.1210.331430.2483290X-RAY DIFFRACTION100
3.121-3.3620.31430.243303X-RAY DIFFRACTION100
3.362-3.70.2591440.2093319X-RAY DIFFRACTION100
3.7-4.2340.2321440.1883332X-RAY DIFFRACTION100
4.234-5.3320.2041460.1593357X-RAY DIFFRACTION100
5.332-35.0480.2261500.1993447X-RAY DIFFRACTION98

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