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- PDB-4g3k: Crystal structure of a. aeolicus nlh1 gaf domain in an inactive state -

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Basic information

Entry
Database: PDB / ID: 4g3k
TitleCrystal structure of a. aeolicus nlh1 gaf domain in an inactive state
ComponentsTranscriptional regulator nlh1
KeywordsTranscription regulator / GAF domain
Function / homology
Function and homology information


sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP 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 / GAF domain ...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 / GAF domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator (NifA family)
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsWemmer, D.E. / Batchelor, J.D. / Wang, A. / Lee, P. / Doucleff, M.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural mechanism of GAF-regulated delta(54) activators from Aquifex aeolicus
Authors: Batchelor, J.D. / Lee, P.S. / Wang, A.C. / Doucleff, M. / Wemmer, D.E.
History
DepositionJul 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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
A: Transcriptional regulator nlh1
B: Transcriptional regulator nlh1


Theoretical massNumber of molelcules
Total (without water)39,6802
Polymers39,6802
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-19 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.350, 119.350, 60.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsThe asymmetric unit contains the biologically relevant dimer.

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Components

#1: Protein Transcriptional regulator nlh1


Mass: 19840.174 Da / Num. of mol.: 2 / Fragment: GAF domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: nlh1, aq_218 / Production host: Escherichia coli (E. coli) / References: UniProt: O66591
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 293 K / pH: 6.2
Details: 32.5% PEG 3350, 250 mM NaCl, and 50 mM MES pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115872 Å / Relative weight: 1
ReflectionResolution: 3.05→19.914 Å / Num. obs: 8699 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.101
Reflection shellResolution: 3.05→3.13 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.392 / Mean I/σ(I) obs: 1.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→19.91 Å / SU ML: 0.37 / Isotropic thermal model: isotropic / σ(F): 2.01 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 868 10 %
Rwork0.208 --
obs0.212 8681 99.8 %
all-8763 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.81 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.3505 Å20 Å20 Å2
2---4.3505 Å20 Å2
3---9.7326 Å2
Refinement stepCycle: LAST / Resolution: 3.05→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 0 0 3 2310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022338
X-RAY DIFFRACTIONf_angle_d0.5823145
X-RAY DIFFRACTIONf_dihedral_angle_d10.305887
X-RAY DIFFRACTIONf_chiral_restr0.037384
X-RAY DIFFRACTIONf_plane_restr0.002380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0503-3.24060.36511410.30461265X-RAY DIFFRACTION100
3.2406-3.48960.30931390.27561270X-RAY DIFFRACTION100
3.4896-3.83850.30411450.22871291X-RAY DIFFRACTION100
3.8385-4.38880.25321430.19551288X-RAY DIFFRACTION100
4.3888-5.50990.20671460.17151312X-RAY DIFFRACTION100
5.5099-19.91450.19861540.19561387X-RAY DIFFRACTION99

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