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- PDB-5yti: Crystal structure of flagellar hook associated protein-3 (HAP-3: ... -

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Basic information

Entry
Database: PDB / ID: 5yti
TitleCrystal structure of flagellar hook associated protein-3 (HAP-3: Q5ZW61_LEGPH) from Legionella pneumophila
ComponentsFlagellar hook associated protein type 3 FlgL
KeywordsSTRUCTURAL PROTEIN / Flagellar hook associated protein3 / HAP-3 / 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 / 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 type 3 FlgL
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / SAD / Resolution: 2.75 Å
AuthorsLankipalli, S. / Hegde, R.P. / Dey, D. / Almo, S.C. / Ramagopal, U.A.
CitationJournal: To be published
Title: Crystal structure of hook associated protein-3 (HAP-3: Q5ZW61_LEGPH) from Legionella pneumophila
Authors: Lankipalli, S. / Ramagopal, U.A.
History
DepositionNov 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar hook associated protein type 3 FlgL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0532
Polymers44,9411
Non-polymers1121
Water362
1
A: Flagellar hook associated protein type 3 FlgL
hetero molecules

A: Flagellar hook associated protein type 3 FlgL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1064
Polymers89,8812
Non-polymers2252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3620 Å2
ΔGint-20 kcal/mol
Surface area29370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.687, 107.687, 90.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein Flagellar hook associated protein type 3 FlgL


Mass: 44940.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: flgL, lpg1226 / Plasmid: BC-PSGX4(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZW61
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.91 Å3/Da / Density % sol: 57.79 % / Mosaicity: 0.294 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG 400, 0.1M Cadmium Chloride hydrate, 0.1M Sodium Acetate Trihydrate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.75→76.15 Å / Num. obs: 14351 / % possible obs: 100 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.032 / Rrim(I) all: 0.094 / Χ2: 0.884 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.89.10.9386970.7430.3250.9940.876100
2.8-2.858.90.7517040.8460.2630.7970.858100
2.85-2.990.6246950.860.2180.6620.861100
2.9-2.968.90.5516970.9070.1930.5850.861100
2.96-3.0390.4476940.9230.1560.4740.852100
3.03-3.18.90.3617090.9610.1260.3830.847100
3.1-3.178.90.2917130.9660.1020.3090.871100
3.17-3.268.90.257000.980.0870.2650.899100
3.26-3.368.90.1897050.9820.0670.2010.892100
3.36-3.468.80.1687100.9890.0590.1780.989100
3.46-3.598.80.1327110.9920.0470.140.95100
3.59-3.738.80.1187110.9930.0410.1251.089100
3.73-3.98.70.1027110.9940.0360.1081.072100
3.9-4.118.70.0827160.9950.030.0880.961100
4.11-4.368.60.0637160.9970.0230.0670.931100
4.36-4.78.40.0497290.9970.0180.0520.858100
4.7-5.178.10.0467210.9980.0170.0490.7599.9
5.17-5.928.70.057360.9980.0180.0540.792100
5.92-7.468.50.0427550.9980.0150.0450.773100
7.46-507.60.0278210.9990.010.0290.69399.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALEPACKdata scaling
SHELXDEphasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.75→76.15 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.888 / SU B: 36.065 / SU ML: 0.3 / SU R Cruickshank DPI: 0.5507 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.551 / ESU R Free: 0.347
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2884 733 5.1 %RANDOM
Rwork0.2354 ---
obs0.2382 13543 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 153.61 Å2 / Biso mean: 91.848 Å2 / Biso min: 62.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å20 Å2-0 Å2
2---1.46 Å2-0 Å2
3---2.92 Å2
Refinement stepCycle: final / Resolution: 2.75→76.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 1 2 2475
Biso mean--126.03 63.65 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192522
X-RAY DIFFRACTIONr_bond_other_d0.0010.022268
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9693428
X-RAY DIFFRACTIONr_angle_other_deg0.78635288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6175333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.4926.102118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.22615400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0131513
X-RAY DIFFRACTIONr_chiral_restr0.0780.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022883
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02458
LS refinement shellResolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 45 -
Rwork0.359 964 -
all-1009 -
obs--97.58 %
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)
11.5344-0.28170.02117.56933.56941.70820.10340.0583-0.120.21590.0971-0.35530.05680.0559-0.20050.52320.0243-0.14110.0779-0.03420.3583-14.7297-51.452719.6555
20.50030.29370.09640.6459-0.09020.32150.0304-0.3125-0.0696-0.3316-0.04690.1693-0.18770.03830.01640.6239-0.1567-0.18460.41360.0150.2481-21.474-8.062343.057
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 70
2X-RAY DIFFRACTION1A351 - 377
3X-RAY DIFFRACTION2A71 - 350

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