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- PDB-4ii7: Archaellum Assembly ATPase FlaI -

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Basic information

Entry
Database: PDB / ID: 4ii7
TitleArchaellum Assembly ATPase FlaI
ComponentsFlaI ATPase
KeywordsHYDROLASE / Hexamer / ATP/ADP / cytoplasmic / membrane associated
Function / homology
Function and homology information


Neutral Protease; domain 2 - #40 / Beta-Lactamase - #370 / Type II/IV secretion system protein / Type II/IV secretion system protein / Neutral Protease; domain 2 / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich ...Neutral Protease; domain 2 - #40 / Beta-Lactamase - #370 / Type II/IV secretion system protein / Type II/IV secretion system protein / Neutral Protease; domain 2 / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Conserved Archaeal protein
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsReindl, S. / Williams, G.J. / Tainer, J.A.
CitationJournal: Mol.Cell / Year: 2013
Title: Insights into FlaI Functions in Archaeal Motor Assembly and Motility from Structures, Conformations, and Genetics.
Authors: Reindl, S. / Ghosh, A. / Williams, G.J. / Lassak, K. / Neiner, T. / Henche, A.L. / Albers, S.V. / Tainer, J.A.
History
DepositionDec 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FlaI ATPase
B: FlaI ATPase
C: FlaI ATPase
D: FlaI ATPase


Theoretical massNumber of molelcules
Total (without water)235,3424
Polymers235,3424
Non-polymers00
Water0
1
A: FlaI ATPase
B: FlaI ATPase

A: FlaI ATPase
B: FlaI ATPase

A: FlaI ATPase
B: FlaI ATPase


Theoretical massNumber of molelcules
Total (without water)353,0136
Polymers353,0136
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area20330 Å2
ΔGint-34 kcal/mol
Surface area135530 Å2
MethodPISA
2
C: FlaI ATPase
D: FlaI ATPase

C: FlaI ATPase
D: FlaI ATPase

C: FlaI ATPase
D: FlaI ATPase


Theoretical massNumber of molelcules
Total (without water)353,0136
Polymers353,0136
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area19190 Å2
ΔGint-31 kcal/mol
Surface area137030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.018, 130.018, 311.772
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
FlaI ATPase / Conserved Archaeal protein


Mass: 58835.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Gene: 1173, Saci_1173 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4J9L0, EC: 3.6.1.4

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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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 293 K / pH: 7
Details: 100mM HEPES pH 7.0, 22% Polyvinylpyrrolidone K 15, 10 mM CoCl2, 15% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.07
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2009
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 3.59→49.923 Å / Num. obs: 34740 / % possible obs: 99 % / Observed criterion σ(I): 1
Reflection shellResolution: 3.59→3.76 Å / % possible all: 87.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IHQ

4ihq


Resolution: 3.59→49.92 Å / SU ML: 0.59 / σ(F): 1.35 / Phase error: 35.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.306 1987 5.73 %
Rwork0.243 --
obs0.246 34698 99.8 %
all-34731 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.59→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16239 0 0 0 16239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01816562
X-RAY DIFFRACTIONf_angle_d1.62822434
X-RAY DIFFRACTIONf_dihedral_angle_d15.6456276
X-RAY DIFFRACTIONf_chiral_restr0.0972561
X-RAY DIFFRACTIONf_plane_restr0.0062860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.59-3.67830.38191410.31592304X-RAY DIFFRACTION99
3.6783-3.77770.41591460.31372323X-RAY DIFFRACTION100
3.7777-3.88880.37421390.31592330X-RAY DIFFRACTION100
3.8888-4.01430.3871420.30812341X-RAY DIFFRACTION100
4.0143-4.15770.37481420.29552323X-RAY DIFFRACTION100
4.1577-4.32410.35191380.28942369X-RAY DIFFRACTION100
4.3241-4.52080.31681410.2622313X-RAY DIFFRACTION100
4.5208-4.75890.2941370.24462331X-RAY DIFFRACTION100
4.7589-5.05680.29891470.24022357X-RAY DIFFRACTION100
5.0568-5.44680.30981400.23192340X-RAY DIFFRACTION100
5.4468-5.99410.29641450.23032323X-RAY DIFFRACTION100
5.9941-6.85960.32931440.23642365X-RAY DIFFRACTION100
6.8596-8.63510.26361460.22072347X-RAY DIFFRACTION100
8.6351-49.92830.25541390.20132345X-RAY DIFFRACTION99

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