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- PDB-7c7z: Crystal structure of the flagellar junction protein FlgL from Leg... -

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Basic information

Entry
Database: PDB / ID: 7c7z
TitleCrystal structure of the flagellar junction protein FlgL from Legionella pneumophila
ComponentsFlagellar hook-associated protein 3
KeywordsSTRUCTURAL PROTEIN / FlgL / Legionella pneumophila
Function / homology
Function and homology information


bacterial-type flagellum hook / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region
Similarity search - Function
Flagellar hook-associated protein 3 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Flagellar hook-associated protein 3 / Flagellar hook associated protein type 3 FlgL
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsSong, W.S. / Hong, H.J. / Yoon, S.I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural study of the flagellar junction protein FlgL from Legionella pneumophila.
Authors: Song, W.S. / Hong, H.J. / Yoon, S.I.
History
DepositionMay 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellar hook-associated protein 3
B: Flagellar hook-associated protein 3


Theoretical massNumber of molelcules
Total (without water)72,4182
Polymers72,4182
Non-polymers00
Water362
1
A: Flagellar hook-associated protein 3


Theoretical massNumber of molelcules
Total (without water)36,2091
Polymers36,2091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellar hook-associated protein 3


Theoretical massNumber of molelcules
Total (without water)36,2091
Polymers36,2091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-10 kcal/mol
Surface area28240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.133, 108.133, 184.146
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Refine code: 3

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPSERSERAA70 - 16033 - 123
211ASPASPSERSERBB70 - 16033 - 123
121SERSERARGARGAA295 - 348258 - 311
221SERSERARGARGBB295 - 348258 - 311
131LEULEUMETMETAA172 - 184135 - 147
231LEULEUMETMETBB172 - 184135 - 147
112ARGARGGLUGLUAA185 - 294148 - 257
212ARGARGGLUGLUBB185 - 294148 - 257

NCS ensembles :
ID
1
2

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Components

#1: Protein Flagellar hook-associated protein 3


Mass: 36209.133 Da / Num. of mol.: 2 / Fragment: UNP residues 44-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: flgL, C3927_05570, DI026_02135 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2S6F8D1, UniProt: Q5ZW61*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.72 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: PEG 6000, citric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.05→30 Å / Num. obs: 21299 / % possible obs: 99.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 28.9
Reflection shellResolution: 3.05→3.1 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1044 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.5.0109refinement
HKL-2000data processing
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YTI

5yti


Resolution: 3.06→30 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.897 / SU B: 37.49 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1025 -RANDOM
Rwork0.228 ---
obs0.2291 20044 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 129.65 Å2 / Biso mean: 61.8 Å2 / Biso min: 23.02 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å20 Å2
2--1 Å20 Å2
3----2 Å2
Refinement stepCycle: final / Resolution: 3.06→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 0 2 4650
Biso mean---24.18 -
Num. residues----630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224708
X-RAY DIFFRACTIONr_bond_other_d0.0010.022988
X-RAY DIFFRACTIONr_angle_refined_deg1.1171.9576405
X-RAY DIFFRACTIONr_angle_other_deg0.83837366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4735626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.09826.233215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.81915743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2661521
X-RAY DIFFRACTIONr_chiral_restr0.0610.2756
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02853
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1913TIGHT POSITIONAL0.030.05
1997LOOSE POSITIONAL0.035
1913TIGHT THERMAL0.050.5
1997LOOSE THERMAL0.0510
2638TIGHT POSITIONAL0.020.05
2640LOOSE POSITIONAL0.035
2638TIGHT THERMAL0.040.5
2640LOOSE THERMAL0.0810
LS refinement shellResolution: 3.06→3.136 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.326 63 -
Rwork-1436 -
obs--98.55 %
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)
11.2582-0.64690.11643.4082-0.29111.3480.0465-0.05760.2166-0.31910.0069-0.0159-0.0430.2422-0.05350.118-0.02230.00150.07420.02240.3162-39.37913.9580.328
22.16420.3362-1.97544.5424-0.39563.342-0.2268-0.325-0.58650.125-0.03760.08620.81650.20870.26440.28420.0159-0.07360.12410.11770.3608-47.591-12.52221.804
33.6345-0.2484-0.00161.371-0.39772.13490.1489-0.228-0.02290.0555-0.1356-0.2223-0.13540.4705-0.01320.0358-0.0761-0.05610.217200.3087-37.81613.11726.709
43.957-0.3054-0.44433.49750.14693.8399-0.04120.02690.0668-0.5263-0.02520.7360.158-0.60720.06640.1178-0.0699-0.16650.17020.08520.3477-63.8248.3936.847
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 184
2X-RAY DIFFRACTION1A295 - 370
3X-RAY DIFFRACTION2A185 - 294
4X-RAY DIFFRACTION3B47 - 184
5X-RAY DIFFRACTION3B295 - 355
6X-RAY DIFFRACTION4B185 - 294

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