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- PDB-4ihq: Archaellum Assembly ATPase FlaI bound to ADP -

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Basic information

Entry
Database: PDB / ID: 4ihq
TitleArchaellum Assembly ATPase FlaI bound to ADP
ComponentsFlaI ATPase
KeywordsHYDROLASE / Hexamer / ATP/ADP / 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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Conserved Archaeal protein
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: FlaI ATPase
B: FlaI ATPase
C: FlaI ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,96813
Polymers176,3323
Non-polymers1,63610
Water13,799766
1
A: FlaI ATPase
B: FlaI ATPase
C: FlaI ATPase
hetero molecules

A: FlaI ATPase
B: FlaI ATPase
C: FlaI ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,93626
Polymers352,6646
Non-polymers3,27120
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area30580 Å2
ΔGint-107 kcal/mol
Surface area130600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.462, 148.083, 123.631
Angle α, β, γ (deg.)90.00, 131.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein FlaI ATPase / Conserved Archaeal protein


Mass: 58777.391 Da / Num. of mol.: 3 / Fragment: FlaI ATPase / Mutation: E336A
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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Non-polymers , 5 types, 776 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 766 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 293 K / pH: 7.6
Details: 7.5% PEG 335 MME 32.5% ethylene glycol 82 mM imidazole 18 mM malate , pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9797,0.9644
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 16, 2010
RadiationMonochromator: KHOZU DOUBLE FLAT CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.96441
ReflectionResolution: 1.584→50 Å / Num. obs: 170270 / % possible obs: 59 % / Observed criterion σ(I): 1
Reflection shellResolution: 1.58→1.67 Å / % possible all: 64.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXAutoSolmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: MAD / Resolution: 2→45.99 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.214 7730 5.05 %
Rwork0.186 --
obs0.187 152953 99.7 %
all-153518 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12379 0 101 766 13246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812912
X-RAY DIFFRACTIONf_angle_d1.17817544
X-RAY DIFFRACTIONf_dihedral_angle_d15.9244955
X-RAY DIFFRACTIONf_chiral_restr0.0791988
X-RAY DIFFRACTIONf_plane_restr0.0052237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.29092680.25234802X-RAY DIFFRACTION99
2.0227-2.04650.26562740.23944849X-RAY DIFFRACTION100
2.0465-2.07150.26962680.23474749X-RAY DIFFRACTION100
2.0715-2.09770.27262480.23784858X-RAY DIFFRACTION100
2.0977-2.12530.26312500.22364870X-RAY DIFFRACTION100
2.1253-2.15440.25032450.21924834X-RAY DIFFRACTION100
2.1544-2.18520.24442790.20664728X-RAY DIFFRACTION100
2.1852-2.21780.2482650.2134833X-RAY DIFFRACTION100
2.2178-2.25250.23022570.20574845X-RAY DIFFRACTION100
2.2525-2.28940.26912650.20754826X-RAY DIFFRACTION100
2.2894-2.32890.22332660.19994818X-RAY DIFFRACTION100
2.3289-2.37120.22662560.19454814X-RAY DIFFRACTION100
2.3712-2.41680.25522540.20364830X-RAY DIFFRACTION100
2.4168-2.46620.23462550.20364854X-RAY DIFFRACTION100
2.4662-2.51980.22652600.20064823X-RAY DIFFRACTION100
2.5198-2.57840.2492440.2094852X-RAY DIFFRACTION100
2.5784-2.64290.23742630.2024865X-RAY DIFFRACTION100
2.6429-2.71430.24012400.20034819X-RAY DIFFRACTION100
2.7143-2.79420.24692780.20214843X-RAY DIFFRACTION100
2.7942-2.88430.22952570.1994853X-RAY DIFFRACTION100
2.8843-2.98740.23662310.19614828X-RAY DIFFRACTION100
2.9874-3.1070.23782490.19764894X-RAY DIFFRACTION100
3.107-3.24840.21792700.20344830X-RAY DIFFRACTION100
3.2484-3.41960.24682270.19744870X-RAY DIFFRACTION100
3.4196-3.63380.21642460.18684867X-RAY DIFFRACTION99
3.6338-3.91420.19832590.17194800X-RAY DIFFRACTION99
3.9142-4.30780.18462500.16054885X-RAY DIFFRACTION100
4.3078-4.93050.17692740.14654866X-RAY DIFFRACTION100
4.9305-6.20960.2032900.18274858X-RAY DIFFRACTION100
6.2096-46.00710.172420.1654960X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.40820.79190.29542.4145-0.3782.05940.2547-0.7374-0.44540.47060.00970.26230.5492-0.5308-0.22440.5437-0.1436-0.02120.51160.23320.4585-2.971182.0231139.85
22.96660.47391.77462.27720.02773.2464-0.1105-0.63130.3520.1081-0.01890.2761-0.4544-0.73030.07390.25160.12170.05330.4478-0.07240.2656-17.3776210.209116.3683
34.53680.3967-0.1523.3947-0.93912.90750.1681-0.9743-1.31880.1777-0.1963-0.3430.6720.4551-0.0070.52840.1661-0.10210.57480.11670.737237.6922175.4269118.9557
43.71920.37940.37891.3665-0.45682.3944-0.0776-0.34810.32940.21530.0123-0.0568-0.32010.02830.05190.30040.0179-0.04770.1521-0.04850.24621.084208.4081131.5171
52.6204-1.61440.37213.0579-0.15651.75520.09170.2083-0.1921-0.1245-0.0324-0.54880.49220.7987-0.05030.48730.2847-0.06010.7721-0.18730.540943.6897179.986474.2375
62.1202-0.01590.41631.1981-0.14813.1282-0.00450.43350.11880.0287-0.0127-0.2392-0.26430.79680.00560.2237-0.0988-0.03270.480.00690.292639.367207.4961100.4838
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 2:228
2X-RAY DIFFRACTION2chain A and resid 229:513
3X-RAY DIFFRACTION3chain B and resid 2:223
4X-RAY DIFFRACTION4chain B and resid 224:513
5X-RAY DIFFRACTION5chain C and resid 2:223
6X-RAY DIFFRACTION6chain C and resid 224:512

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