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- PDB-4g3w: Crystal structure of a. aeolicus nlh1 gaf domain in an inactive state -

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Basic information

Entry
Database: PDB / ID: 4g3w
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: 2.7 Å
AuthorsBatchelor, J.D. / Wang, A. / Lee, P. / Doucleff, M. / Wemmer, D.E.
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 15, 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


Theoretical massNumber of molelcules
Total (without water)19,3401
Polymers19,3401
Non-polymers00
Water32418
1
A: Transcriptional regulator nlh1

A: Transcriptional regulator nlh1


Theoretical massNumber of molelcules
Total (without water)38,6792
Polymers38,6792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1540 Å2
ΔGint-17 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.780, 59.780, 106.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a dimer generated from the asymmetric unit by the operation y, x, -z.

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Components

#1: Protein Transcriptional regulator nlh1


Mass: 19339.674 Da / Num. of mol.: 1 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 0.2M Na/K phosphate, 0.1M Bis Tris propane pH 7.5, and 20% PEG 3350, 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 14, 2009
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115872 Å / Relative weight: 1
ReflectionResolution: 2.68→20 Å / Num. obs: 5719 / % possible obs: 95 %

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.85 Å / SU ML: 0.31 / σ(F): 1.99 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 254 4.59 %
Rwork0.204 --
obs0.206 5539 97.3 %
all-5719 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.53 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.3483 Å20 Å20 Å2
2--10.3483 Å2-0 Å2
3----20.6966 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 0 18 1104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161107
X-RAY DIFFRACTIONf_angle_d1.6531488
X-RAY DIFFRACTIONf_dihedral_angle_d15.325422
X-RAY DIFFRACTIONf_chiral_restr0.079171
X-RAY DIFFRACTIONf_plane_restr0.008182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7004-3.39940.31531310.24462613X-RAY DIFFRACTION99
3.3994-19.85460.20461230.18712672X-RAY DIFFRACTION96

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