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- PDB-3jzz: Crystal structure of Pseudomonas aeruginosa (strain: Pa110594) ty... -

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Basic information

Entry
Database: PDB / ID: 3jzz
TitleCrystal structure of Pseudomonas aeruginosa (strain: Pa110594) typeIV pilin in space group P212121
ComponentsType IV pilin structural subunit
KeywordsSTRUCTURAL PROTEIN / Pilin / PilA / Pilus / Methylation
Function / homology
Function and homology information


pilus / cell adhesion
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: 1.597 Å
AuthorsNguyen, Y. / Jackson, S.G. / Aidoo, F. / Junop, M.S. / Burrows, L.L.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural characterization of Novel Pseudomonas aeruginosa type IV pilins.
Authors: Nguyen, Y. / Jackson, S.G. / Aidoo, F. / Junop, M. / Burrows, L.L.
History
DepositionSep 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 1.3Nov 20, 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: Type IV pilin structural subunit


Theoretical massNumber of molelcules
Total (without water)15,1291
Polymers15,1291
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.460, 44.869, 88.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Type IV pilin structural subunit


Mass: 15128.734 Da / Num. of mol.: 1 / Fragment: UNP residues 34-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: Pa110594 / Gene: pilA / Plasmid: D-TOPO-pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami(DE3) / References: UniProt: Q8KQ36
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 1.94 Å3/Da / Density % sol: 36.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 20% w/v PEG 1000, 8% v/v Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 13, 2009
Details: double-crystal monochromator Si(111), beam focused by a toroidal mirror
RadiationMonochromator: Si(111) channel-cut crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.597→50 Å / Num. all: 16182 / Num. obs: 16182 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 31.5

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Processing

Software
NameClassification
CBASSdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3JYZ

3jyz


Resolution: 1.597→27.966 Å / SU ML: 0.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 1608 9.99 %Random
Rwork0.1796 ---
all0.1842 16182 --
obs0.1842 16094 98.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.19 Å2 / ksol: 0.35 e/Å3
Refinement stepCycle: LAST / Resolution: 1.597→27.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1068 0 0 217 1285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0231086
X-RAY DIFFRACTIONf_angle_d1.8911491
X-RAY DIFFRACTIONf_dihedral_angle_d15.874372
X-RAY DIFFRACTIONf_chiral_restr0.084188
X-RAY DIFFRACTIONf_plane_restr0.006194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.597-1.64840.26911370.17041243X-RAY DIFFRACTION96
1.6484-1.70730.24851430.14761291X-RAY DIFFRACTION99
1.7073-1.77570.21031420.14981288X-RAY DIFFRACTION98
1.7757-1.85650.24761470.15371307X-RAY DIFFRACTION98
1.8565-1.95430.21031450.15881296X-RAY DIFFRACTION99
1.9543-2.07680.21361460.17191304X-RAY DIFFRACTION100
2.0768-2.2370.25081480.17271331X-RAY DIFFRACTION100
2.237-2.4620.22781480.18641330X-RAY DIFFRACTION100
2.462-2.8180.23051480.18681333X-RAY DIFFRACTION100
2.818-3.54930.20461500.16961352X-RAY DIFFRACTION100
3.5493-27.9660.18811540.18651411X-RAY DIFFRACTION97

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