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- PDB-2px3: Crystal structure of FlhF complexed with GTP/Mg(2+) -

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Basic information

Entry
Database: PDB / ID: 2px3
TitleCrystal structure of FlhF complexed with GTP/Mg(2+)
ComponentsFlagellar biosynthesis protein flhF
KeywordsBIOSYNTHETIC PROTEIN / SRP GTPase / flagellum / protein transport
Function / homology
Function and homology information


bacterial-type flagellum organization / signal recognition particle binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting / protein transport / GTPase activity / GTP binding / identical protein binding / plasma membrane
Similarity search - Function
Flagellar FlhF biosynthesis protein, N domain / Flagellar biosynthesis protein FlhF / : / 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 ...Flagellar FlhF biosynthesis protein, N domain / Flagellar biosynthesis protein FlhF / : / 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
GUANOSINE-5'-TRIPHOSPHATE / Flagellar biosynthesis protein FlhF
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBange, G. / Wild, K. / Sinning, I.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: The crystal structure of the third signal-recognition particle GTPase FlhF reveals a homodimer with bound GTP.
Authors: Bange, G. / Petzold, G. / Wild, K. / Parlitz, R.O. / Sinning, I.
History
DepositionMay 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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
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_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.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_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_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
Revision 1.3Apr 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: Flagellar biosynthesis protein flhF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9803
Polymers33,4321
Non-polymers5472
Water543
1
A: Flagellar biosynthesis protein flhF
hetero molecules

A: Flagellar biosynthesis protein flhF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9596
Polymers66,8642
Non-polymers1,0954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)80.965, 80.965, 126.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsOne monomer per asymmetric unit. The second monomer of the dimer is generated by the crystallographic two-fold axis.

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Components

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


Mass: 33432.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: flhF / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q01960
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10-13 % (w/v) PEG6000, 4% (v/v) 2-methyl-2,4-pentanediol, 0.1 M MOPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2004 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→68.2 Å / Num. obs: 7364 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rsym value: 0.088 / Net I/σ(I): 19.4
Reflection shellResolution: 3.2→3.31 Å / Mean I/σ(I) obs: 4.2 / Rsym value: 0.408 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: G domain of FtsY from Sulfolobus solfataricus

Resolution: 3.2→49.76 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.31 374 -random
Rwork0.25 ---
all-7384 --
obs-7359 99.7 %-
Displacement parametersBiso mean: 49.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3.2→49.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 33 3 2059
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.067
RfactorNum. reflection% reflection
Rfree0.489 53 -
Rwork0.349 --
obs-1121 98.1 %

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