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- PDB-1ay2: STRUCTURE OF THE FIBER-FORMING PROTEIN PILIN AT 2.6 ANGSTROMS RES... -

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Entry
Database: PDB / ID: 1ay2
TitleSTRUCTURE OF THE FIBER-FORMING PROTEIN PILIN AT 2.6 ANGSTROMS RESOLUTION
ComponentsTYPE 4 PILIN
KeywordsCELL ADHESION / TYPE IV PILIN / FIBER-FORMING PROTEIN / MEMBRANE PROTEIN / DNA INDING PROTEIN / CONTRACTILE PROTEIN
Function / homologyFimbrial protein pilin / Prokaryotic N-terminal methylation site / Pilin (bacterial filament) / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site. / pilus / cell adhesion / Fimbrial protein
Function and homology information
Specimen sourceNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / 2.6 Å resolution
AuthorsForest, K.T. / Parge, H.E. / Tainer, J.A.
CitationJournal: Nature / Year: 1995
Title: Structure of the fibre-forming protein pilin at 2.6 A resolution.
Authors: Parge, H.E. / Forest, K.T. / Hickey, M.J. / Christensen, D.A. / Getzoff, E.D. / Tainer, J.A.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 13, 1997 / Release: Apr 29, 1998
RevisionDateData content typeGroupProviderType
1.0Apr 29, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYPE 4 PILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9515
Polyers17,2071
Non-polymers7454
Water2,324129
1
A: TYPE 4 PILIN
hetero molecules

A: TYPE 4 PILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,90210
Polyers34,4132
Non-polymers1,4898
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
γ
α
β
Length a, b, c (Å)127.580, 121.080, 26.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC 2 2 2

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide TYPE 4 PILIN / FIMBRIAE


Mass: 17206.504 Da / Num. of mol.: 1 / Source: (natural) Neisseria gonorrhoeae (bacteria) / Cellular location: EXTRACELLULAR / Organelle: PILUS / Strain: MS11 / References: UniProt: P02974

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Non-polymers , 5 types, 133 molecules

#2: Chemical ChemComp-GLA / ALPHA D-GALACTOSE


Mass: 180.156 Da / Num. of mol.: 1 / Formula: C6H12O6
#3: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6 / N-Acetylglucosamine
#4: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Formula: Pt / Platinum
#5: Chemical ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 1 / Formula: C7H16O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Formula: H2O / Water

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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: 3.16 / Density percent sol: 6 %
Crystal growpH: 8
Details: PROTEIN WAS CRYSTALLIZED FROM 60% PEG400, 50 MM CHESS, PH 8.0, 1% BETA-OCTYL GLUCOSIDE, 0.6% 1,2,3-HEPTANETRIOL.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Parge, H.E., (1990) J. Biol. Chem., 265, 2278.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
11 %(w/v)protein1drop
21-1.5 %BOG1drop
3100 mMTris-HCl1drop
420 mM1dropNaCl
51 mMdithiothreitol1drop
60.02 %1dropNaN3
736-45 %PEG4001drop
8100 mMTris-HCl1reservoir
9reservoir1drop
100.02 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 290 kelvins
SourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.07
DetectorType: MARRESEARCH / Details: BENT MIRROR / Detector: IMAGE PLATE / Collection date: May 1, 1993
RadiationMonochromator: SI(111) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionD resolution high: 2.6 Å / D resolution low: 24 Å / Number obs: 6494 / Observed criterion sigma I: 2 / Rsym value: 0.081 / NetI over sigmaI: 6.7 / Redundancy: 4 % / Percent possible obs: 95
Reflection shellHighest resolution: 2.6 Å / Lowest resolution: 2.78 Å / MeanI over sigI obs: 2.3 / Rsym value: 0.307 / Redundancy: 4.2 % / Percent possible all: 80.2
Reflection
*PLUS
Rmerge I obs: 0.081

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
AGROVATAdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATA)data scaling
X-PLOR3.1phasing
RefineMethod to determine structure: MIR
Details: SOLVENT FLATTENING (WITH 50%) SOLVENT) USING PHASES WAS USED TO IMPROVE PHASES (F.O.M. INCREASED FROM 0.75 - 0.86) FOR FITTING. DATA FROM A PT-SOAKED DERIVATIVE CRYSTAL WAS USED FOR REFINEMENT BECAUSE IT WAS STRONGER THAN "NATIVE" DATA. THE EXPECTED N-TERMINAL METHYL-PHE WAS VERIFIED BY N-TERMINAL SEQUENCING BUT WAS NOT INCLUDED IN THE MODEL BECAUSE IT WAS NOT APPARENT IN ELECTRON DENSITY. WATERS WERE NOT RESTRAINED DURING REFINEMENT AND TWO WATERS (333 AND 348) MOVED CLOSE TO THE PT SITE.
Data cutoff high absF: 1 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Sigma F: 2
Displacement parametersB iso mean: 3 Å2 / Aniso B11: -4.25 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 8.25 Å2 / Aniso B23: 0 Å2 / Aniso B33: -4 Å2
Least-squares processR factor R work: 0.194 / R factor obs: 0.194 / Highest resolution: 2.6 Å / Lowest resolution: 1 Å / Number reflection obs: 6565 / Percent reflection obs: 95
Refine analyzeLuzzati d res low obs: 1 Å
Refine hist #LASTHighest resolution: 2.6 Å / Lowest resolution: 1 Å
Number of atoms included #LASTProtein: 1208 / Nucleic acid: 0 / Ligand: 36 / Solvent: 129 / Total: 1373
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.359
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2.0
X-RAY DIFFRACTIONx_scbond_it2.0
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS shellHighest resolution: 2.6 Å / R factor R work: 0.324 / Lowest resolution: 2.72 Å / Number reflection R work: 723 / Total number of bins used: 8
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM_AUX.PROTOPH3.CHO
X-RAY DIFFRACTION3PARAM3_MOD.CHOHEPT123.TOP
X-RAY DIFFRACTION4TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.359

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