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- PDB-9en1: FliG interacting domain of SpFlhF (FID) -

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Basic information

Entry
Database: PDB / ID: 9en1
TitleFliG interacting domain of SpFlhF (FID)
ComponentsFlagellar biosynthesis protein FlhF
KeywordsSIGNALING PROTEIN / Flagellation / Flagellar assembly / GTPase
Function / homology
Function and homology information


bacterial-type flagellum organization / signal recognition particle binding / SRP-dependent cotranslational protein targeting to membrane / protein transport / GTPase activity / GTP binding / ATP hydrolysis activity / plasma membrane
Similarity search - Function
Flagellar biosynthesis protein FlhF / : / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Flagellar biosynthesis protein FlhF
Similarity search - Component
Biological speciesShewanella putrefaciens CN-32 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsDornes, A. / Mais, C.-N. / Bange, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)495924434 Germany
CitationJournal: To Be Published
Title: FlhF-directed assembly of a polar flagellum
Authors: Dornes, A. / Schmidt, L.M. / Mais, C.-N. / Hook, J.C. / Kressler, D. / Thormann, K. / Bange, G.
History
DepositionMar 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellar biosynthesis protein FlhF
B: Flagellar biosynthesis protein FlhF
C: Flagellar biosynthesis protein FlhF
D: Flagellar biosynthesis protein FlhF
E: Flagellar biosynthesis protein FlhF
F: Flagellar biosynthesis protein FlhF
G: Flagellar biosynthesis protein FlhF
H: Flagellar biosynthesis protein FlhF
I: Flagellar biosynthesis protein FlhF
J: Flagellar biosynthesis protein FlhF
K: Flagellar biosynthesis protein FlhF
L: Flagellar biosynthesis protein FlhF


Theoretical massNumber of molelcules
Total (without water)70,47512
Polymers70,47512
Non-polymers00
Water00
1
A: Flagellar biosynthesis protein FlhF
B: Flagellar biosynthesis protein FlhF


Theoretical massNumber of molelcules
Total (without water)11,7462
Polymers11,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Flagellar biosynthesis protein FlhF
I: Flagellar biosynthesis protein FlhF


Theoretical massNumber of molelcules
Total (without water)11,7462
Polymers11,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Flagellar biosynthesis protein FlhF
F: Flagellar biosynthesis protein FlhF


Theoretical massNumber of molelcules
Total (without water)11,7462
Polymers11,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Flagellar biosynthesis protein FlhF
K: Flagellar biosynthesis protein FlhF


Theoretical massNumber of molelcules
Total (without water)11,7462
Polymers11,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
G: Flagellar biosynthesis protein FlhF
L: Flagellar biosynthesis protein FlhF


Theoretical massNumber of molelcules
Total (without water)11,7462
Polymers11,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
H: Flagellar biosynthesis protein FlhF
J: Flagellar biosynthesis protein FlhF


Theoretical massNumber of molelcules
Total (without water)11,7462
Polymers11,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.530, 106.530, 106.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Flagellar biosynthesis protein FlhF / Flagella-associated GTP-binding protein


Mass: 5872.892 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria)
Gene: Sputcn32_2561 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4Y8J9
Has protein modificationN

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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: 4.29 Å3/Da / Density % sol: 71.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6M Sodium citrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97699 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97699 Å / Relative weight: 1
ReflectionResolution: 3.01→37.68 Å / Num. obs: 23814 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.08 / Net I/σ(I): 18.63
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.01-3.082.77817200.4082.8841
3.08-3.172.31117090.5222.3991
3.17-3.261.39916920.7011.4531
3.26-3.360.8415960.980.8731
3.36-3.470.55515580.9430.5771
3.47-3.590.41215560.9590.4311
3.59-3.730.29814550.9850.311
3.73-3.880.2313830.9920.2391
3.88-4.050.15513450.9950.1611
4.05-4.250.10413140.9980.1081
4.25-4.480.0812230.9980.0831
4.48-4.750.0711650.9990.0731
4.75-5.080.06111090.9990.0631
5.08-5.490.0629910.9980.0651
5.49-6.010.0629510.9990.0641
6.01-6.720.0658510.9990.0681
6.72-7.760.0447750.9990.0451
7.76-9.50.0376420.9990.0391
9.5-13.440.03649910.0371
13.44-37.680.0422800.9980.0441

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→37.68 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2684 1186 4.99 %
Rwork0.2347 --
obs0.2365 23766 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.01→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 0 0 0 4203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034302
X-RAY DIFFRACTIONf_angle_d0.5825728
X-RAY DIFFRACTIONf_dihedral_angle_d4.81585
X-RAY DIFFRACTIONf_chiral_restr0.048675
X-RAY DIFFRACTIONf_plane_restr0.002718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.01-3.140.40281490.3762823X-RAY DIFFRACTION99
3.14-3.310.40341460.33582779X-RAY DIFFRACTION100
3.31-3.510.30071470.26772814X-RAY DIFFRACTION99
3.51-3.790.32531490.2782828X-RAY DIFFRACTION100
3.79-4.170.29021460.24422787X-RAY DIFFRACTION100
4.17-4.770.25641500.20312843X-RAY DIFFRACTION100
4.77-60.28311490.2332828X-RAY DIFFRACTION100
6-37.680.22491500.21782878X-RAY DIFFRACTION99
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)
15.6724-4.52721.70546.71312.99146.89810.3808-0.53461.265-0.3029-0.560.4613-0.4501-0.44410.0621.3326-0.05020.01670.9071-0.0430.698548.0775-47.45362.0368
24.1926-0.37044.35816.8115-1.52089.1316-0.0334-0.23150.9710.0130.08111.10050.8430.66630.1651.04290.08890.12621.5037-0.13530.595358.0142-53.2092-10.8724
34.2141-0.3467-2.00727.95365.53994.54910.17160.28670.13641.089-0.485-0.1210.6144-0.47210.00790.5578-0.0424-0.08711.14690.08371.468513.6999-74.1358-6.5759
41.7218-2.9674-0.60266.7191-0.35176.2401-0.00220.6251-0.4528-1.05220.03280.2943-1.2453-0.2188-0.03480.4531-0.04130.12841.271-0.18791.420840.3085-74.98-17.1379
59.1881-0.00840.85242.4765-4.17677.41570.7395-0.2296-0.53060.0957-0.5504-1.46080.3988-0.03730.0471.38130.03240.07850.5288-0.09711.659732.2051-80.265115.7941
62.31060.09540.79066.5430.66076.0238-0.0996-1.0405-0.4764-0.3803-0.67310.0840.7533-0.0150.29940.64120.04790.05091.6625-0.06481.52353.9179-80.0636-6.2471
79.5231-1.83173.64987.10532.42973.98130.07190.79960.0294-2.2599-0.3713-0.2806-0.26881.0637-0.10411.62950.0369-0.00270.73620.09081.443327.1401-106.91469.7743
87.1813-0.48113.65157.5331.07518.48180.8411-1.2688-0.92720.2453-0.35660.60970.53591.1674-0.03011.0267-0.21280.09871.4421-0.10240.52995.911-107.1442-11.4774
92.9525-1.90160.69053.7468-0.74628.4432-0.47680.2797-1.4532-0.57670.71870.22490.11430.3908-0.30270.6063-0.02110.03621.26880.05761.83327.0302-85.3118-11.7913
108.9919-4.31513.85046.9586-0.24848.1949-0.5148-0.37260.59380.65570.38051.29910.14630.16070.08871.0597-0.138-0.0411.18520.08810.6785-5.6345-101.68551.5452
115.4093-0.7224.55737.9192-4.89037.8276-0.45360.6395-0.2865-0.405-0.2552-0.2604-0.0802-0.32740.44531.0761-0.080.14360.4988-0.07171.445721.1016-67.343510.7451
125.67990.7897-4.89512.76720.75167.86520.6382-0.53220.71220.6033-0.2842-0.8859-0.5535-0.7443-0.24441.2965-0.0035-0.11140.55650.1011.320721.723-93.520120.861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 45)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 48)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 46)
4X-RAY DIFFRACTION4(chain 'D' and resid 0 through 45)
5X-RAY DIFFRACTION5(chain 'E' and resid 0 through 47)
6X-RAY DIFFRACTION6(chain 'F' and resid 0 through 48)
7X-RAY DIFFRACTION7(chain 'G' and resid 1 through 48)
8X-RAY DIFFRACTION8(chain 'H' and resid 1 through 47)
9X-RAY DIFFRACTION9(chain 'I' and resid 1 through 48)
10X-RAY DIFFRACTION10(chain 'J' and resid 1 through 46)
11X-RAY DIFFRACTION11(chain 'K' and resid 0 through 46)
12X-RAY DIFFRACTION12(chain 'L' and resid 1 through 46)

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