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- PDB-1x6z: Structure 1: cryocooled crystal structure of the truncated pak pi... -

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Basic information

Entry
Database: PDB / ID: 1x6z
TitleStructure 1: cryocooled crystal structure of the truncated pak pilin from Pseudomonas aeruginosa at 0.78A 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.78 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 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2013Group: 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 13, 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
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.244, 37.244, 147.856
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.: 232 / 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 Å3/Da / Density % sol: 38.7 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.65 Å
DetectorType: SBC-2 / Detector: CCD / Date: Sep 12, 1999
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65 Å / Relative weight: 1
ReflectionResolution: 0.78→36.04 Å / Num. all: 107451 / Num. obs: 107451 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.86 % / Biso Wilson estimate: 6.8 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 5.47
Reflection shellResolution: 0.78→0.79 Å / % possible all: 41.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0001refinement
d*TREKdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DZO

1dzo


Resolution: 0.78→36.04 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.391 / SU ML: 0.011 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.013 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1535 5428 5 %RANDOM
Rwork0.14194 ---
all0.14252 107451 --
obs0.14252 107451 100 %-
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: 10.641 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 0.78→36.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms863 0 0 232 1095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022915
X-RAY DIFFRACTIONr_bond_other_d0.0020.02850
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.9671239
X-RAY DIFFRACTIONr_angle_other_deg1.02132006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2855118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02725.31232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.97315171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.201155
X-RAY DIFFRACTIONr_chiral_restr0.1530.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02993
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02158
X-RAY DIFFRACTIONr_nbd_refined0.2510.2172
X-RAY DIFFRACTIONr_nbd_other0.1920.2871
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.2555
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2131
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3230.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2360.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.246
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.7621.5625
X-RAY DIFFRACTIONr_mcbond_other0.5181.5245
X-RAY DIFFRACTIONr_mcangle_it2.3292970
X-RAY DIFFRACTIONr_scbond_it3.2233341
X-RAY DIFFRACTIONr_scangle_it4.2344.5269
X-RAY DIFFRACTIONr_rigid_bond_restr1.1831897
X-RAY DIFFRACTIONr_sphericity_free14.8845232
X-RAY DIFFRACTIONr_sphericity_bonded3.22751751
LS refinement shellResolution: 0.78→0.788 Å / Total num. of bins used: 50 /
RfactorNum. reflection
Rfree0.407 54
Rwork0.411 1320

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