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- PDB-4g3v: Crystal structure of A. Aeolicus nlh2 gaf domain in an inactive state -

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Basic information

Entry
Database: PDB / ID: 4g3v
TitleCrystal structure of A. Aeolicus nlh2 gaf domain in an inactive state
ComponentsTranscriptional regulator nlh2
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, conserved site / Sigma-54 interaction domain C-terminal part 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 ...Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part 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 (NtrC family)
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBatchelor, J.D. / Lee, P. / Wang, A. / 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Transcriptional regulator nlh2
B: Transcriptional regulator nlh2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9576
Polymers38,8152
Non-polymers1424
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-51 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.450, 65.450, 128.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe asymmetric unit contains the biologically relevant dimer.

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Components

#1: Protein Transcriptional regulator nlh2


Mass: 19407.598 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: nlh2, aq_1792 / Production host: Escherichia coli (E. coli) / References: UniProt: O67661
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.05 Å3/Da / Density % sol: 39.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22% PEG 550 monomethyl ether, 150mM MgCl2, and 100mM HEPES pH 7.0, 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 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2007
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115872 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 35851 / Num. obs: 35725 / % possible obs: 99.6 % / Redundancy: 10.67 % / Rmerge(I) obs: 0.042

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Processing

Software
NameVersionClassification
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.163 Å / SU ML: 0.2 / σ(F): 1.99 / Phase error: 19.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 1947 5.45 %RANDOM
Rwork0.1626 ---
obs0.165 35719 99.73 %-
all-35849 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.463 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7143 Å2-0 Å2-0 Å2
2---2.7143 Å20 Å2
3---5.4286 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 4 169 2743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072646
X-RAY DIFFRACTIONf_angle_d0.9693560
X-RAY DIFFRACTIONf_dihedral_angle_d11.3411000
X-RAY DIFFRACTIONf_chiral_restr0.055410
X-RAY DIFFRACTIONf_plane_restr0.003443
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.7001-1.74260.32771400.254323572364100
1.7426-1.78960.26981390.206823792665100
1.7896-1.84230.24651340.174323922401100
1.8423-1.90170.24971390.164223872558100
1.9017-1.96960.21371350.153823852613100
1.9696-2.04840.21390.140723822578100
2.0484-2.14150.20321400.135123992435100
2.1415-2.25420.1591420.125324192513100
2.2542-2.39520.18311390.129723782697100
2.3952-2.57970.21691380.136824332234100
2.5797-2.83860.20711370.148824582844100
2.8386-3.24760.22461390.156924152556100
3.2476-4.08510.19261430.160624852618100
4.0851-19.16450.20441430.19222503264797

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