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- PDB-4s3l: Crystal Structure of major pilin protein PitB from type II pilus ... -

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Basic information

Entry
Database: PDB / ID: 4s3l
TitleCrystal Structure of major pilin protein PitB from type II pilus of Streptococcus pneumoniae
ComponentsMajor Pilin Protein
KeywordsCELL ADHESION / Major pilin / Type II pilus / virulence / CNAB / IgG fold / IgG-rev fold / Pilin protein
Function / homologySpy0128-like isopeptide containing domain / Streptococcal pilin isopeptide linker superfamily / : / Domain of unknown function (DUF7601) / Domain of unknown function (DUF5979) / membrane / PitB
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsShaik, M.M. / Dessen, A. / Di Guilmi, A.M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: A Structural Snapshot of Type II Pilus Formation in Streptococcus pneumoniae.
Authors: Shaik, M.M. / Lombardi, C. / Maragno Trindade, D. / Fenel, D. / Schoehn, G. / Di Guilmi, A.M. / Dessen, A.
History
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Oct 7, 2015Group: Database references
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major Pilin Protein
B: Major Pilin Protein


Theoretical massNumber of molelcules
Total (without water)74,3962
Polymers74,3962
Non-polymers00
Water1,42379
1
A: Major Pilin Protein


Theoretical massNumber of molelcules
Total (without water)37,1981
Polymers37,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Major Pilin Protein


Theoretical massNumber of molelcules
Total (without water)37,1981
Polymers37,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.210, 54.210, 361.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Major Pilin Protein


Mass: 37197.891 Da / Num. of mol.: 2 / Fragment: UNP residues 46-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (strain Taiwan19F-14) (bacteria)
Strain: Taiwan19F-14 / Gene: pitB / Plasmid: pet151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3FNT1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 3.57 Å3/Da / Density % sol: 65.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 3M NaCl, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.939
SYNCHROTRONESRF BM1420.939
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 315r1CCDOct 13, 2013mirrors
MARMOSAIC 225 mm CCD2CCDJan 23, 2014mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1channel cut ESRF monochromatorSINGLE WAVELENGTHMx-ray1
2Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.8→54.21 Å / Num. obs: 25595 / % possible obs: 80 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.195 / Net I/σ(I): 5.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
autoSHARPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→54.21 Å / SU ML: 0.58 / σ(F): 1.35 / Phase error: 39.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2977 1281 5.08 %
Rwork0.2393 --
obs0.2422 25228 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→54.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5194 0 0 79 5273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015290
X-RAY DIFFRACTIONf_angle_d1.3397188
X-RAY DIFFRACTIONf_dihedral_angle_d16.9111942
X-RAY DIFFRACTIONf_chiral_restr0.089828
X-RAY DIFFRACTIONf_plane_restr0.007942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.91210.46721420.37862616X-RAY DIFFRACTION97
2.9121-3.04460.3921250.34592668X-RAY DIFFRACTION98
3.0446-3.20510.3511480.29452665X-RAY DIFFRACTION99
3.2051-3.40590.33031400.24872624X-RAY DIFFRACTION99
3.4059-3.66880.30841320.24422692X-RAY DIFFRACTION99
3.6688-4.03790.32871560.22682629X-RAY DIFFRACTION99
4.0379-4.6220.24581400.18512678X-RAY DIFFRACTION100
4.622-5.82210.24341480.18842680X-RAY DIFFRACTION100
5.8221-54.22010.2391500.21682695X-RAY DIFFRACTION100

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