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- PDB-3syn: Crystal structure of FlhF in complex with its activator -

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Basic information

Entry
Database: PDB / ID: 3syn
TitleCrystal structure of FlhF in complex with its activator
Components
  • ATP-binding protein YlxH
  • Flagellar biosynthesis protein flhF
KeywordsPROTEIN TRANSPORT / SRP GTPASE / FLAGELLUM / BIOSYNTHETIC PROTEIN / GTPase ACTIVATING PROTEIN / Type 3 secretion system / GTP-binding protein
Function / homology
Function and homology information


bacterial-type flagellum organization / signal recognition particle binding / negative regulation of cell division / SRP-dependent cotranslational protein targeting to membrane / protein targeting / cytoplasmic side of plasma membrane / protein transport / GTPase activity / GTP binding / ATP hydrolysis activity ...bacterial-type flagellum organization / signal recognition particle binding / negative regulation of cell division / SRP-dependent cotranslational protein targeting to membrane / protein targeting / cytoplasmic side of plasma membrane / protein transport / GTPase activity / GTP binding / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Flagellar FlhF biosynthesis protein, N domain / Flagellar biosynthesis protein FlhF / : / Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 / NUBPL iron-transfer P-loop NTPase / ATP binding protein MinD/FleN / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Flagellar FlhF biosynthesis protein, N domain / Flagellar biosynthesis protein FlhF / : / Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 / NUBPL iron-transfer P-loop NTPase / ATP binding protein MinD/FleN / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / Flagellum site-determining protein YlxH / Flagellar biosynthesis protein FlhF
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.063 Å
AuthorsBange, G. / Kuemmerer, N. / Wild, K. / Sinning, I.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structural basis for the molecular evolution of SRP-GTPase activation by protein.
Authors: Bange, G. / Kummerer, N. / Grudnik, P. / Lindner, R. / Petzold, G. / Kressler, D. / Hurt, E. / Wild, K. / Sinning, I.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Flagellar biosynthesis protein flhF
B: Flagellar biosynthesis protein flhF
C: Flagellar biosynthesis protein flhF
D: Flagellar biosynthesis protein flhF
E: ATP-binding protein YlxH
F: ATP-binding protein YlxH
G: ATP-binding protein YlxH
H: ATP-binding protein YlxH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,75735
Polymers145,1108
Non-polymers3,64727
Water1,63991
1
A: Flagellar biosynthesis protein flhF
E: ATP-binding protein YlxH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,30910
Polymers36,2782
Non-polymers1,0328
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-75 kcal/mol
Surface area13550 Å2
MethodPISA
2
B: Flagellar biosynthesis protein flhF
F: ATP-binding protein YlxH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1178
Polymers36,2782
Non-polymers8406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-51 kcal/mol
Surface area13490 Å2
MethodPISA
3
C: Flagellar biosynthesis protein flhF
G: ATP-binding protein YlxH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2139
Polymers36,2782
Non-polymers9367
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-68 kcal/mol
Surface area13770 Å2
MethodPISA
4
D: Flagellar biosynthesis protein flhF
H: ATP-binding protein YlxH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1178
Polymers36,2782
Non-polymers8406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-37 kcal/mol
Surface area13520 Å2
MethodPISA
5
A: Flagellar biosynthesis protein flhF
B: Flagellar biosynthesis protein flhF
E: ATP-binding protein YlxH
F: ATP-binding protein YlxH
hetero molecules

C: Flagellar biosynthesis protein flhF
D: Flagellar biosynthesis protein flhF
G: ATP-binding protein YlxH
H: ATP-binding protein YlxH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,75735
Polymers145,1108
Non-polymers3,64727
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_444x-1,y-1,z-11
Buried area21150 Å2
ΔGint-370 kcal/mol
Surface area42920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.790, 63.360, 114.500
Angle α, β, γ (deg.)92.26, 100.96, 94.25
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 109:366 )
211chain B and (resseq 109:366 )
311chain C and (resseq 109:366 )
411chain D and (resseq 109:366 )
112chain E and (resseq 6:21 )
212chain F and (resseq 6:21 )
312chain G and (resseq 6:21 )
412chain H and (resseq 6:21 )

NCS ensembles :
ID
1
2

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

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


Mass: 33432.180 Da / Num. of mol.: 4 / Fragment: unp residues 79-366
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: flhF, BSU16400 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q01960
#2: Protein/peptide
ATP-binding protein YlxH


Mass: 2845.371 Da / Num. of mol.: 4 / Fragment: unp residues 1-23 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria) / References: UniProt: P40742

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Non-polymers , 5 types, 118 molecules

#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF3
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris, 1.8 M Ammoniumsulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.06→63.1 Å / Num. all: 26278 / Num. obs: 25016 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rsym value: 0.088 / Net I/σ(I): 8.5
Reflection shellResolution: 3.06→3.23 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 5 / Rsym value: 0.225 / % possible all: 93.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2PX3

2px3


Resolution: 3.063→63.091 Å / SU ML: 0.45 / σ(F): 0.06 / Phase error: 22.75 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 1237 5.07 %random
Rwork0.1809 ---
obs0.1838 24400 92.86 %-
all-26278 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.348 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.8369 Å2-3.5196 Å20.426 Å2
2---0.222 Å2-5.3299 Å2
3----5.615 Å2
Refinement stepCycle: LAST / Resolution: 3.063→63.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8712 0 207 91 9010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099052
X-RAY DIFFRACTIONf_angle_d1.20612230
X-RAY DIFFRACTIONf_dihedral_angle_d20.753372
X-RAY DIFFRACTIONf_chiral_restr0.0761396
X-RAY DIFFRACTIONf_plane_restr0.0041516
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2042X-RAY DIFFRACTIONPOSITIONAL
12B2042X-RAY DIFFRACTIONPOSITIONAL0.049
13C2042X-RAY DIFFRACTIONPOSITIONAL0.04
14D2042X-RAY DIFFRACTIONPOSITIONAL0.051
21E136X-RAY DIFFRACTIONPOSITIONAL
22F136X-RAY DIFFRACTIONPOSITIONAL0.041
23G136X-RAY DIFFRACTIONPOSITIONAL0.036
24H136X-RAY DIFFRACTIONPOSITIONAL0.04
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.063-3.18570.31831290.24212443X-RAY DIFFRACTION87
3.1857-3.33070.30491360.21892521X-RAY DIFFRACTION91
3.3307-3.50620.25591390.18612561X-RAY DIFFRACTION93
3.5062-3.72590.22181510.16692598X-RAY DIFFRACTION94
3.7259-4.01350.21281350.15562628X-RAY DIFFRACTION95
4.0135-4.41730.21791390.14362630X-RAY DIFFRACTION96
4.4173-5.05630.17261240.14272648X-RAY DIFFRACTION95
5.0563-6.36940.23831410.17772608X-RAY DIFFRACTION94
6.3694-63.10460.22611430.19652526X-RAY DIFFRACTION92

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