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- PDB-1qve: Crystal structure of the truncated K122-4 pilin from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 1qve
TitleCrystal structure of the truncated K122-4 pilin from Pseudomonas aeruginosa
ComponentsFimbrial protein
KeywordsCELL ADHESION / Type IV Pilin / Lectin / Adhesin / Pseudomonas
Function / homology
Function and homology information


type IV pilus / type IV pilus-dependent motility / glycosphingolipid binding / biological process involved in interaction with host / periplasmic space / cell adhesion / membrane
Similarity search - Function
Glycoprotein, Type 4 Pilin / Glycoprotein, Type 4 Pilin / Fimbrial protein pilin / Pilin (bacterial filament) / : / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsAudette, G.F. / Irvin, R.T. / Hazes, B.
Citation
Journal: Biochemistry / Year: 2004
Title: Crystallographic Analysis of the Pseudomonas aeruginosa Strain K122-4 Monomeric Pilin Reveals a Conserved Receptor-Binding Architecture
Authors: Audette, G.F. / Irvin, R.T. / Hazes, B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Purification, crystallization and preliminary diffraction studies of the Pseudomonas aeruginosa strain K122-4 monomeric pilin
Authors: Audette, G.F. / Irvin, R.T. / Hazes, B.
History
DepositionAug 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / struct_ref_seq_dif
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.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). FOR AN EXPLANATION OF THE BIOLOGICAL UNIT, PLEASE REFER TO THE FOLLOWING REFERENCES: Parge, H.E., Forest, K.T., Hickey, M.J., Christensen, D.A., Getzoff, E.D., Tainer, J.A.: Structure of the fibre-forming protein pilin at 2.6 A resolution. Nature 378 pp. 32 (1995). Keizer, D.W., Slupsky, C.M., Kalisiak, M., Campbell, A.P., Crump, M.P., Sastry, P.A., Hazes, B., Irvin, R.T., Sykes, B.D.: Structure of a Pilin Monomer from Pseudomonas Aeruginosa. Implications for the Assembly of Pili. J.Biol.Chem. 276 pp. 24186 (2001).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fimbrial protein
B: Fimbrial protein


Theoretical massNumber of molelcules
Total (without water)25,6912
Polymers25,6912
Non-polymers00
Water5,206289
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.184, 38.930, 37.228
Angle α, β, γ (deg.)66.39, 111.11, 93.74
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 6 / Auth seq-ID: 32 - 147 / Label seq-ID: 8 - 123

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsType IV pilins are initially produced as integral inner membrane proteins that are subsequently assembled into a helical fiber. The dimer present in our P1 unit cell is not believed to reflect a biological complex.

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Components

#1: Protein Fimbrial protein / Pilin / Strain K122-4


Mass: 12845.372 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: K122-4 / Gene: PILA OR FIMA / Plasmid: pMAL-p2X / Production host: Escherichia coli (E. coli) / Strain (production host): ER2507 / References: UniProt: P17838
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 1.93 Å3/Da / Density % sol: 36.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, Potassium Phosphate Monobasic, Sodium Cacodylate, Tris HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 4, 2003
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.54→37 Å / Num. obs: 26457 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.059 / Net I/σ(I): 16.5
Reflection shellResolution: 1.54→1.61 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 6.6 / Num. unique all: 2260 / Rsym value: 0.096 / % possible all: 88.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1AYZ

1ayz


Resolution: 1.54→35.58 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.398 / SU ML: 0.052 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17855 1336 5 %RANDOM
Rwork0.13905 ---
obs0.14112 25365 93.92 %-
all-25635 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.229 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0 Å20.01 Å2
3----0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.197 Å
Refinement stepCycle: LAST / Resolution: 1.54→35.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 0 289 2078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211813
X-RAY DIFFRACTIONr_bond_other_d0.0020.021622
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9582470
X-RAY DIFFRACTIONr_angle_other_deg0.83533808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022014
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02312
X-RAY DIFFRACTIONr_nbd_refined0.230.2323
X-RAY DIFFRACTIONr_nbd_other0.2480.21793
X-RAY DIFFRACTIONr_nbtor_other0.0860.21131
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2170
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3180.2105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0531.51244
X-RAY DIFFRACTIONr_mcangle_it1.56921999
X-RAY DIFFRACTIONr_scbond_it2.223569
X-RAY DIFFRACTIONr_scangle_it3.2554.5471
X-RAY DIFFRACTIONr_rigid_bond_restr1.13621813
X-RAY DIFFRACTIONr_sphericity_free3.9422289
X-RAY DIFFRACTIONr_sphericity_bonded1.84521789
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1516 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.475
loose thermal0.8810
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 86 -
Rwork0.156 1810 -
obs-1810 90.6 %
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)
11.23983.59281.822915.72657.32223.7765-0.11380.09440.1118-0.21990.08630.2974-0.13580.03250.02750.04330.0183-0.02330.0530.01380.0751-3.12561.0584-2.0565
25.19755.9622-0.047911.85920.20732.42330.0107-0.21980.15540.2442-0.18160.35350.0954-0.19960.17080.095-0.00460.02430.0616-0.02730.0395-1.67164.608112.358
31.1240.0693-0.06872.93160.23221.54190.0513-0.0002-0.02170.0164-0.06360.0638-0.0108-0.01670.01230.01350.0179-0.00510.024-0.00860.01931.9231-0.2290.6223
41.19060.64360.06639.26283.851910.4551-0.20860.2024-0.0829-0.4524-0.06980.34590.0831-0.30690.27840.0444-0.02440.02330.0523-0.02480.09114.4804-5.7545-9.4574
533.1636-2.1431-19.97542.96470.525611.02040.5032-0.97450.5984-0.1041-0.1419-0.2244-0.21420.5828-0.36130.1059-0.0338-0.00570.0864-0.02780.024317.6419-3.6957-16.1415
62.25972.2281-3.52555.4257-8.013614.9610.0862-0.0593-0.10120.0585-0.3763-0.2611-0.06370.55750.29010.02230.0172-0.00050.10770.02790.079918.567735.21468.7707
72.1689-2.08230.839613.6612-4.01634.81290.06840.2288-0.1184-0.1302-0.24690.00760.50190.47690.17840.15090.04820.04630.1158-0.01380.039216.267131.4796-5.1993
81.63240.8947-0.57334.2234-2.62683.69670.0619-0.0948-0.0091-0.0676-0.1192-0.09640.10090.24230.05730.01420.0153-0.00210.0626-0.01690.020513.063235.9916.7321
91.70060.55081.8944.16250.09295.8162-0.0034-0.3922-0.04160.3615-0.2039-0.0675-0.10430.25790.20730.06950.00190.00190.1139-0.00310.05028.941939.158917.7793
1011.9484-9.3253-8.932912.10039.96089.57470.25770.70450.1564-0.1284-0.51820.1166-0.1685-0.49620.26050.1035-0.01570.0030.0741-0.00850.03831.752249.601519.8211
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA25 - 541 - 30
2X-RAY DIFFRACTION2AA55 - 7231 - 48
3X-RAY DIFFRACTION3AA73 - 12849 - 104
4X-RAY DIFFRACTION4AA129 - 142105 - 118
5X-RAY DIFFRACTION5AA143 - 150119 - 126
6X-RAY DIFFRACTION6BB25 - 541 - 30
7X-RAY DIFFRACTION7BB55 - 7231 - 48
8X-RAY DIFFRACTION8BB73 - 12849 - 104
9X-RAY DIFFRACTION9BB129 - 142105 - 118
10X-RAY DIFFRACTION10BB143 - 149119 - 125

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