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- PDB-1x6y: Structure 6: room temperature crystal structure of the truncated ... -

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Basic information

Entry
Database: PDB / ID: 1x6y
TitleStructure 6: room temperature crystal structure of the truncated pak pilin from Pseudomonas aeruginosa at 1.80A resolution
ComponentsFimbrial protein
KeywordsSTRUCTURAL PROTEIN / TYPE IV PILIN / LECTIN / ADHESIN
Function / homology
Function and homology information


type IV pilus / type IV pilus-dependent motility / 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 / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsDunlop, K.V. / Irvin, R.T. / Hazes, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Pros and cons of cryocrystallography: should we also collect a room-temperature data set?
Authors: Dunlop, K.V. / Irvin, R.T. / Hazes, B.
History
DepositionAug 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Dec 7, 2016Group: Other
Revision 1.4Aug 23, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fimbrial protein


Theoretical massNumber of molelcules
Total (without water)12,6961
Polymers12,6961
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.814, 37.814, 149.437
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsProtein assembles to form a fiber. See PDB codes 1DZO and 1AY2.

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Components

#1: Protein Fimbrial protein / Pilin / Strain PAK


Mass: 12696.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: K / Cellular location: EXTRACELLULAR FILAMENTOUS APPENDAGE / Gene: pilA, fimA / Plasmid: PRLD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02973
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.2
Details: 60% Ammonium Sulfate, 0.1M Hepes, pH 8.2, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 10, 2001 / Details: SUPPER MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.55→20.8 Å / Num. all: 10797 / Num. obs: 10797 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 30 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 14.62
Reflection shellResolution: 1.8→1.85 Å / % possible all: 62.1

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Processing

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

1dzo


Resolution: 1.55→20.8 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.222 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.066 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.172 837 5.2 %RANDOM
Rwork0.14502 ---
all0.1464 10797 --
obs0.1464 10797 94.6 %-
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: 11.207 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.55→20.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 0 143 989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021877
X-RAY DIFFRACTIONr_bond_other_d0.0020.02804
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9691194
X-RAY DIFFRACTIONr_angle_other_deg1.05931884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5995119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02975
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02150
X-RAY DIFFRACTIONr_nbd_refined0.2080.2156
X-RAY DIFFRACTIONr_nbd_other0.2460.2902
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.2524
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 54
Rwork0.346 780
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)
11.1914-1.4005-1.96651.99972.81893.82290.01410.0158-0.05690.0196-0.02270.036-0.02390.00310.00860.07380.01160.00510.0641-0.0080.05667.6244.91747.553
21.6708-0.2172-0.55890.93331.17840.2623-0.06280.1298-0.00930.01370.07850.0439-0.04360.014-0.01560.0620.0094-0.00790.07370.00110.06664.6141.58931.835
30.266-0.1291-0.51080.48870.26810.5001-0.0150.03170.03590.01120.0188-0.0237-0.02780.0148-0.00380.05820.0228-0.00780.0841-0.01010.057911.34511.43744.062
46.0521-2.0784-1.13862.7562-1.25912.7654-0.232-0.3350.09020.24770.1083-0.1661-0.15-0.01310.12370.07970.025-0.03430.0888-0.02190.016914.02213.67257.696
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 54
2X-RAY DIFFRACTION2A55 - 79
3X-RAY DIFFRACTION3A80 - 133
4X-RAY DIFFRACTION4A134 - 144

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