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- PDB-4oq1: Structure of the Streptococcal ancillary pilin -

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Basic information

Entry
Database: PDB / ID: 4oq1
TitleStructure of the Streptococcal ancillary pilin
ComponentsCell wall surface anchor family protein
KeywordsCELL ADHESION / CnaB domain / IgG-rev fold / pilin protein
Function / homology
Function and homology information


membrane => GO:0016020 / extracellular region / membrane
Similarity search - Function
Immunoglobulin-like - #4180 / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cell wall surface anchor family protein / Cell wall surface anchor family protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsShaik, M.M. / Di Guilmi, A.M. / Dessen, A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis of Pilus Anchoring by the Ancillary Pilin RrgC of Streptococcus pneumoniae.
Authors: Shaik, M.M. / Maccagni, A. / Tourcier, G. / Di Guilmi, A.M. / Dessen, A.
History
DepositionFeb 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Jul 2, 2014Group: Database references
Revision 1.3Nov 6, 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 / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell wall surface anchor family protein


Theoretical massNumber of molelcules
Total (without water)41,9701
Polymers41,9701
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.580, 65.760, 60.420
Angle α, β, γ (deg.)90.00, 110.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cell wall surface anchor family protein / Ancillary pilin


Mass: 41970.109 Da / Num. of mol.: 1 / Fragment: UNP residues 22-368 / Mutation: E179A/K180A/E181A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-334 / TIGR4 / Gene: SP0464, SP_0464 / Plasmid: pLIM01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q97SC1, UniProt: A0A0H2UNM0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 1.92 Å3/Da / Density % sol: 35.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris, 28% w/v PEG2000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.97923
SYNCHROTRONESRF ID14-421.0045
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELFeb 4, 2013
ADSC QUANTUM 315r2CCDFeb 18, 2013
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1channel-cut Si(111)SINGLE WAVELENGTHMx-ray1
2channel-cut Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979231
21.00451
ReflectionResolution: 1.85→34.63 Å / Num. all: 26430 / Num. obs: 26430 / % possible obs: 80 % / Observed criterion σ(F): 2.91 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 7.1
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 3 / % possible all: 96.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SHARPphasing
PHENIXrefinerefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→34.63 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.949 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23692 1328 5 %RANDOM
Rwork0.18552 ---
obs0.1882 25102 96.75 %-
all-26430 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.917 Å2
Baniso -1Baniso -2Baniso -3
1-3.58 Å2-0 Å20.01 Å2
2---0.43 Å2-0 Å2
3----2.43 Å2
Refinement stepCycle: LAST / Resolution: 1.85→34.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 0 237 2884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.0220.0192698
X-RAY DIFFRACTIONf_bond_other_d0.0020.022574
X-RAY DIFFRACTIONf_angle_refined_deg21.9593659
X-RAY DIFFRACTIONf_angle_other_deg0.9335922
X-RAY DIFFRACTIONf_dihedral_angle_1_deg8.075329
X-RAY DIFFRACTIONf_dihedral_angle_2_deg34.61624.488127
X-RAY DIFFRACTIONf_dihedral_angle_3_deg13.65915475
X-RAY DIFFRACTIONf_dihedral_angle_4_deg11.4791516
X-RAY DIFFRACTIONf_chiral_restr0.130.2420
X-RAY DIFFRACTIONf_gen_planes_refined0.0110.023029
X-RAY DIFFRACTIONf_gen_planes_other0.0010.02609
X-RAY DIFFRACTIONf_nbd_refined
X-RAY DIFFRACTIONf_nbd_other
X-RAY DIFFRACTIONf_nbtor_refined
X-RAY DIFFRACTIONf_nbtor_other
X-RAY DIFFRACTIONf_xyhbond_nbd_refined
X-RAY DIFFRACTIONf_xyhbond_nbd_other
X-RAY DIFFRACTIONf_metal_ion_refined
X-RAY DIFFRACTIONf_metal_ion_other
X-RAY DIFFRACTIONf_symmetry_vdw_refined
X-RAY DIFFRACTIONf_symmetry_vdw_other
X-RAY DIFFRACTIONf_symmetry_hbond_refined
X-RAY DIFFRACTIONf_symmetry_hbond_other
X-RAY DIFFRACTIONf_symmetry_metal_ion_refined
X-RAY DIFFRACTIONf_symmetry_metal_ion_other
X-RAY DIFFRACTIONf_mcbond_it3.1282.6821322
X-RAY DIFFRACTIONf_mcbond_other3.1282.6771321
X-RAY DIFFRACTIONf_mcangle_it4.4283.9991649
X-RAY DIFFRACTIONf_mcangle_other4.4274.0051650
X-RAY DIFFRACTIONf_scbond_it4.033.1641376
X-RAY DIFFRACTIONf_scbond_other4.0293.1691377
X-RAY DIFFRACTIONf_scangle_it
X-RAY DIFFRACTIONf_scangle_other6.0594.5732011
X-RAY DIFFRACTIONf_long_range_B_refined8.2922.5653064
X-RAY DIFFRACTIONf_long_range_B_other8.21622.3252993
X-RAY DIFFRACTIONf_rigid_bond_restr
X-RAY DIFFRACTIONf_sphericity_free
X-RAY DIFFRACTIONf_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 108 -
Rwork0.25 1835 -
obs--95.62 %

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