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- PDB-6t8s: Structure of the major Type IV pilin PilA1 from Clostridium difficile -

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Basic information

Entry
Database: PDB / ID: 6t8s
TitleStructure of the major Type IV pilin PilA1 from Clostridium difficile
ComponentsPilin
KeywordsPROTEIN FIBRIL / Pillin / Type IV Pillin
Function / homologyBacterial general secretion pathway protein G-type pilin / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / protein secretion by the type II secretion system / Prokaryotic N-terminal methylation site / type II protein secretion system complex / membrane => GO:0016020 / Pilin
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.65 Å
AuthorsCrawshaw, A.D. / Basle, A. / Salgado, P.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
MedicalMR/M000923/1 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: A practical overview of molecular replacement: Clostridioides difficile PilA1, a difficult case study.
Authors: Crawshaw, A.D. / Basle, A. / Salgado, P.S.
History
DepositionOct 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Pilin
BBB: Pilin
CCC: Pilin


Theoretical massNumber of molelcules
Total (without water)47,7333
Polymers47,7333
Non-polymers00
Water4,576254
1
AAA: Pilin


Theoretical massNumber of molelcules
Total (without water)15,9111
Polymers15,9111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Pilin


Theoretical massNumber of molelcules
Total (without water)15,9111
Polymers15,9111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Pilin


Theoretical massNumber of molelcules
Total (without water)15,9111
Polymers15,9111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.570, 102.570, 104.336
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Pilin


Mass: 15910.838 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria)
Gene: pilE1, SAMEA840506_01547, SAMEA897066_02999, SAMEA897109_03172, SAMEA897162_02309
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A449M2W4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.65→73.25 Å / Num. obs: 67404 / % possible obs: 100 % / Redundancy: 14.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.037 / Rrim(I) all: 0.14 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.65-1.6811.73.6843977933960.391.1423.8620.6100
8.89-73.1413.40.04771215330.9990.0130.04941.199.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
DIALSdata reduction
Aimlessdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.65→73.25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.204 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.082
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 3423 5.1 %RANDOM
Rwork0.1941 ---
obs0.1952 63905 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 116.35 Å2 / Biso mean: 26.4 Å2 / Biso min: 15.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.65→73.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2995 0 0 254 3249
Biso mean---34.38 -
Num. residues----400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133142
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172963
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.6344291
X-RAY DIFFRACTIONr_angle_other_deg1.3051.5846964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6895429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24228.142113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35415574
X-RAY DIFFRACTIONr_chiral_restr0.0490.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023537
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02499
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 220 -
Rwork0.337 4684 -
all-4904 -
obs--99.94 %

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