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- PDB-5fhy: Crystal structure of FliD (HAP2) from Pseudomonas aeruginosa PAO1 -

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Basic information

Entry
Database: PDB / ID: 5fhy
TitleCrystal structure of FliD (HAP2) from Pseudomonas aeruginosa PAO1
ComponentsB-type flagellar hook-associated protein 2
KeywordsSTRUCTURAL PROTEIN / bacterial flagella / cap protein
Function / homology
Function and homology information


bacterial-type flagellum filament cap / bacterial-type flagellum hook / bacterial-type flagellum-dependent cell motility / cell adhesion / extracellular region
Similarity search - Function
Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / Flagellin hook, IN motif / Flagellin hook IN motif
Similarity search - Domain/homology
B-type flagellar hook-associated protein 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsPostel, S. / Bonsor, D. / Diederichs, K. / Sundberg, E.J.
CitationJournal: Elife / Year: 2016
Title: Bacterial flagellar capping proteins adopt diverse oligomeric states.
Authors: Postel, S. / Deredge, D. / Bonsor, D.A. / Yu, X. / Diederichs, K. / Helmsing, S. / Vromen, A. / Friedler, A. / Hust, M. / Egelman, E.H. / Beckett, D. / Wintrode, P.L. / Sundberg, E.J.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B-type flagellar hook-associated protein 2
B: B-type flagellar hook-associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8205
Polymers71,7512
Non-polymers693
Water1,58588
1
B: B-type flagellar hook-associated protein 2
hetero molecules
x 6
A: B-type flagellar hook-associated protein 2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)430,92330
Polymers430,50912
Non-polymers41418
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation5_565y,-x+y+1,z1
crystal symmetry operation6_655x-y+1,x,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_764-y+2,x-y+1,z-11
crystal symmetry operation3_674-x+y+1,-x+2,z-11
crystal symmetry operation4_774-x+2,-y+2,z-11
crystal symmetry operation5_564y,-x+y+1,z-11
crystal symmetry operation6_654x-y+1,x,z-11
Buried area34660 Å2
ΔGint-338 kcal/mol
Surface area120200 Å2
MethodPISA
2
A: B-type flagellar hook-associated protein 2
B: B-type flagellar hook-associated protein 2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)430,92330
Polymers430,50912
Non-polymers41418
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation5_565y,-x+y+1,z1
crystal symmetry operation6_655x-y+1,x,z1
Buried area22440 Å2
ΔGint-283 kcal/mol
Surface area132420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.741, 124.741, 107.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein B-type flagellar hook-associated protein 2 / HAP2 / Filament cap protein / Flagellar cap protein


Mass: 35875.734 Da / Num. of mol.: 2 / Fragment: UNP residues 78-405
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: fliD, PA1094 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pLysS / References: UniProt: Q9K3C5
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.35 Å3/Da / Density % sol: 63.28 % / Description: hexagonal thick plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystallized in 0.8 M NaK Tartrate, 0.1 M Hepes pH 7.5 using random matrix microseed screening
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 8, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.2→62.4 Å / Num. all: 367311 / Num. obs: 47974 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 60.67 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 17.15
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.5 % / Rmerge(I) obs: 3.702 / Mean I/σ(I) obs: 0.55 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: low resolution SeMet protein

Resolution: 2.201→62.371 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 38.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2867 4594 4.92 %random
Rwork0.2492 ---
obs0.251 47968 98.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.201→62.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 3 88 3219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043149
X-RAY DIFFRACTIONf_angle_d0.9554287
X-RAY DIFFRACTIONf_dihedral_angle_d11.2841077
X-RAY DIFFRACTIONf_chiral_restr0.033551
X-RAY DIFFRACTIONf_plane_restr0.003561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2006-2.22570.45921380.40972919X-RAY DIFFRACTION94
2.2257-2.25180.38551530.42212908X-RAY DIFFRACTION98
2.2518-2.27930.40141510.41372937X-RAY DIFFRACTION98
2.2793-2.30820.41651580.40552927X-RAY DIFFRACTION99
2.3082-2.33850.39441510.4042977X-RAY DIFFRACTION98
2.3385-2.37060.43951610.39012910X-RAY DIFFRACTION99
2.3706-2.40440.38641510.37622952X-RAY DIFFRACTION99
2.4044-2.44030.371700.36652921X-RAY DIFFRACTION98
2.4403-2.47850.42051580.36512983X-RAY DIFFRACTION99
2.4785-2.51910.37321270.34722921X-RAY DIFFRACTION99
2.5191-2.56250.37451590.35443000X-RAY DIFFRACTION99
2.5625-2.60910.35171420.35122999X-RAY DIFFRACTION99
2.6091-2.65930.35741800.33352885X-RAY DIFFRACTION99
2.6593-2.71360.3631470.34272981X-RAY DIFFRACTION99
2.7136-2.77260.37591550.3292995X-RAY DIFFRACTION99
2.7726-2.83710.37591320.32362972X-RAY DIFFRACTION99
2.8371-2.9080.33021440.31732959X-RAY DIFFRACTION99
2.908-2.98670.30761750.28472933X-RAY DIFFRACTION99
2.9867-3.07450.33311600.27782934X-RAY DIFFRACTION99
3.0745-3.17380.30861490.26943011X-RAY DIFFRACTION99
3.1738-3.28720.31951640.26372938X-RAY DIFFRACTION99
3.2872-3.41880.30431320.25922988X-RAY DIFFRACTION99
3.4188-3.57440.3061440.24813011X-RAY DIFFRACTION99
3.5744-3.76280.31311920.2342904X-RAY DIFFRACTION99
3.7628-3.99850.2691720.23312981X-RAY DIFFRACTION99
3.9985-4.30720.21381570.19952977X-RAY DIFFRACTION99
4.3072-4.74050.2331410.18752980X-RAY DIFFRACTION100
4.7405-5.42610.26031380.20613009X-RAY DIFFRACTION100
5.4261-6.8350.22331660.22432974X-RAY DIFFRACTION100
6.835-62.39550.24291270.2083025X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.44246.0343-1.26888.2976-1.67421.91450.5859-0.9005-0.020.945-0.893-0.29570.0450.17930.22040.4121-0.06-0.13580.49170.0010.40638.2286132.152174.294
25.0713-3.7484-2.30777.8732.06353.4410.3618-0.40160.45150.1167-0.26430.005-0.53290.0212-0.0980.5423-0.0079-0.14880.5557-0.08980.882756.455161.729272.6929
36.79844.53371.0836.9736-0.16195.4146-0.51480.49761.7714-1.02360.531.0227-0.5031-0.1099-0.02380.53810.0161-0.16560.59930.12351.067651.2266161.434365.6534
46.26963.10920.61464.4665-0.19560.5212-0.13570.18260.3386-0.2161-0.12040.2791-0.14560.05910.16130.4031-0.0045-0.15520.45520.00660.380341.466137.809568.4069
54.9568-0.4486-6.7861-0.02640.52659.2161-0.5512-0.6508-0.4550.832-0.28070.39473.25030.16250.84931.4907-0.44660.0430.84840.16870.601927.8606120.064498.0901
67.01247.47866.91147.9667.36546.808-2.0087-0.19351.0446-2.36740.86120.2189-2.49831.07420.55441.95760.06610.44471.69160.17650.436229.1673119.5451130.2256
77.2656-3.54410.61664.1541.63831.5871-0.18410.90230.102-0.11460.4753-0.15150.382-0.1236-0.32280.9811-0.0973-0.11390.87220.09080.54980.5687136.924237.5367
84.67760.5448-0.37942.39671.3634.8623-0.12970.35830.6796-0.1610.10630.2399-0.7323-0.39860.04170.82570.1049-0.11520.78580.25940.781957.6323161.882741.1524
98.7509-3.4701-0.65072.13580.20370.94780.3310.81970.2721-0.6052-0.18090.06560.0581-0.0753-0.18251.0742-0.1817-0.13220.80490.12750.542777.029140.516942.7611
100.97671.4202-0.45641.7621-0.67120.4924-0.1901-1.041-0.42940.68480.1016-0.6561-0.8967-0.66720.12021.59630.2396-0.05831.2946-0.08850.674494.5681126.5426-2.0341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 80 through 109 )
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 180 )
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 212 )
4X-RAY DIFFRACTION4chain 'A' and (resid 213 through 268 )
5X-RAY DIFFRACTION5chain 'A' and (resid 269 through 296 )
6X-RAY DIFFRACTION6chain 'A' and (resid 297 through 308 )
7X-RAY DIFFRACTION7chain 'B' and (resid 80 through 109 )
8X-RAY DIFFRACTION8chain 'B' and (resid 110 through 212 )
9X-RAY DIFFRACTION9chain 'B' and (resid 213 through 273 )
10X-RAY DIFFRACTION10chain 'B' and (resid 274 through 308 )

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