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- PDB-1dzo: Truncated PAK pilin from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 1dzo
TitleTruncated PAK pilin from Pseudomonas aeruginosa
ComponentsTYPE IV PILIN
KeywordsCELL ADHESION / LECTIN / ADHESIN
Function / homology
Function and homology information


pilus / 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 PAK (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.63 Å
AuthorsHazes, B. / Read, R.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal Structure of Pseudomonas Aeruginosa Pak Pilin Suggests a Main-Chain-Dominated Mode of Receptor Binding
Authors: Hazes, B. / Sastry, P.A. / Hayakawa, K. / Read, R.J. / Irvin, R.T.
History
DepositionMar 6, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2000Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Remark 650 HELIX DETERMINATION METHOD: DSSP

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYPE IV PILIN


Theoretical massNumber of molelcules
Total (without water)12,6961
Polymers12,6961
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.114, 38.114, 149.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsON CELLS PILIN IS FOUND AS LONG THIN FIBERS WHICH MEDIATE CELL ATTACHMENT. BASED ON MOLECULAR MODELING A PRELIMINARY FIBER MODEL HAS BEEN PROPOSED FOR THE RELATED TYPE IV PILIN OF NEISSERIA GONORRHOEAE(PDB ID CODE 1AY2). TO GENERATE THE CORRESPONDING MODEL FOR PAK PILIN THE COORDINATES IN THIS ENTRY SHOULD BE SUPERIMPOSED ON THE NEISSERIA MODEL FOLLOWED BY THE APPLICATION OF THE TRANSFORMATIONS AS INDICATED IN PDB ENTRY 1AY2.PDB ALTHOUGH THE NEISSERIA MODEL IS THE BEST CURRENT MODEL FOR THE FIBER STRUCTURE, IT SHOULD BE KEPT IN MIND THAT SIGNIFICANT DEVIATIONS FROM REALITY MAY EXIST. IN PARTICULAR, IT MAY BE POSSIBLE TO CREATE A SIMILAR MODEL BY STACKING PERFECT PENTAMERS OF PILIN MOLECULES. THE TYPE IV PILUS IS POLAR AND IT APPEARS TO EXPOSE EXTREMELY HYDROPHOBIC ALPHA HELICES AT ONE OF ITS ENDS. BASED ON RECEPTOR BINDING CONSIDERATIONS WE HAVE PROPOSED THAT THE HYDROPHOBIC ALPHA HELICES ARE DISPLAYED AT THE TIP OF THE PILUS AND THEREFORE INTERACT WITH HOST CELLS. THIS CONTRASTS WITH EARLIER MODELS WHERE THE HELICES WERE ASSUMED TO BE BURIED IN THE BACTERIAL OUTER MEMBRANE.

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Components

#1: Protein TYPE IV PILIN


Mass: 12696.225 Da / Num. of mol.: 1 / Fragment: GLOBULAR DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAK (bacteria)
Description: RESIDUES 22-28 ARE FROM THE EXPRESSION VECTOR. RESIDUES 29-144 ARE FROM THE MATURE PROTEIN.
Cellular location: EXTRACELLULAR FILAMENTOUS APPENDAGE / Gene: PILA / Plasmid: PRLD / Cellular location (production host): PERIPLASMIC SPACE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P02973
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A IS A DELETION MUTANT, MISSING RESIDUES 1-28 OF THE NATIVE SEQUENCE. THE RECOMBINANT PROTEIN ...CHAIN A IS A DELETION MUTANT, MISSING RESIDUES 1-28 OF THE NATIVE SEQUENCE. THE RECOMBINANT PROTEIN CONTAINS 7 N-TERMINAL RESIDUES DERIVED FROM THE EXPRESSION VECTOR. THE FIRST 3 HAVE NO DENSITY, THE OTHER FOUR HAVE BEEN MODELED AS RESIDUES 25 - 28 RESIDUES 128 - 144 FORM A DISULPHIDE BONDED LOOP (THE DSL) WHICH CONTAINS THE RECEPTOR BINDING SITE.
Sequence detailsRESIDUES 22-28 ARE FROM THE EXPRESSION VECTOR. RESIDUES 22-24 HAVE NOT BEEN MODELED DUE TO LACK OF ...RESIDUES 22-28 ARE FROM THE EXPRESSION VECTOR. RESIDUES 22-24 HAVE NOT BEEN MODELED DUE TO LACK OF ELECTRON DENSITY

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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: 2.14 Å3/Da / Density % sol: 43 %
Description: DERIVATIVE DATA WERE SCALED USING THE NATIVE DATA AS A REFERENCE
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.2
Details: HANGING DROP USING 1 ML OF RESERVOIR DROPS MADE FROM 3 MICROLITRE PROTEIN AND 3 MICROLITRE OF MOTHER LIQUOR PROTEIN SOLUTION = 10 MG/ML IN WATER MOTHER LIQUOR = 60% (NH4)2SO4, 0.1M HEPES PH 8.2
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
260 %ammonium sulfate11
30.1 MHEPES11
460 %ammonium sulfate12
50.1 MHEPES12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 2000 / Details: SUPPER MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.633→37.44 Å / Num. obs: 253714 / % possible obs: 99.5 % / Redundancy: 7.6 % / Biso Wilson estimate: 16.8 Å2 / Rsym value: 0.049 / Net I/σ(I): 26.7
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 10.1 / Rsym value: 0.19 / % possible all: 96.4
Reflection
*PLUS
Num. obs: 14500 / Num. measured all: 110628 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 96.4 % / Rmerge(I) obs: 0.19

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
ARP/wARPphasing
DMphasing
SOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.63→37.44 Å / SU B: 1.26 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.08
Details: CNS EXPLICIT BULK SOLVENT CORRECTION WAS USED. B-SPHERE RMS = 1.851 FOR FREE ATOMS AND 2.429 FOR BONDED ATOMS
RfactorNum. reflection% reflectionSelection details
Rfree0.181 750 5.2 %RANDOM
Rwork0.153 ---
obs-14500 99.5 %-
Displacement parametersBiso mean: 16.3 Å2
Refinement stepCycle: LAST / Resolution: 1.63→37.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 0 131 977
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0230.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0280.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.63299
X-RAY DIFFRACTIONp_mcangle_it3.48899
X-RAY DIFFRACTIONp_scbond_it4.38199
X-RAY DIFFRACTIONp_scangle_it6.16499
X-RAY DIFFRACTIONp_plane_restr0.01640.03
X-RAY DIFFRACTIONp_chiral_restr0.1340.15
X-RAY DIFFRACTIONp_singtor_nbd0.1761
X-RAY DIFFRACTIONp_multtor_nbd0.2641
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.0881
X-RAY DIFFRACTIONp_planar_tor2.73
X-RAY DIFFRACTIONp_staggered_tor10.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.920
X-RAY DIFFRACTIONp_special_tor

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