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- PDB-3rgu: Structure of Fap-NRa at pH 5.0 -

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Basic information

Entry
Database: PDB / ID: 3rgu
TitleStructure of Fap-NRa at pH 5.0
ComponentsFimbriae-associated protein Fap1
KeywordsSTRUCTURAL PROTEIN / HELICAL BUNDLE / CELL WALL / PEPTIDOGLYCAN-ANCHOR / ADHESION / DENTAL CARIES / pH
Function / homology
Function and homology information


pilus / cell adhesion / extracellular region / cytoplasm
Similarity search - Function
Protein of unknown function DUF445 / Protein of unknown function (DUF445) / Serine-rich repeat adhesion glycoprotein / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Immunoglobulin FC, subunit C / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Protein of unknown function DUF445 / Protein of unknown function (DUF445) / Serine-rich repeat adhesion glycoprotein / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Immunoglobulin FC, subunit C / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
alpha-D-glucopyranose / Fap1 adhesin / Fap1 adhesin
Similarity search - Component
Biological speciesStreptococcus parasanguinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGarnett, J.A. / Matthews, S.J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: Structural insight into the role of Streptococcus parasanguinis Fap1 within oral biofilm formation.
Authors: Garnett, J.A. / Simpson, P.J. / Taylor, J. / Benjamin, S.V. / Tagliaferri, C. / Cota, E. / Chen, Y.Y. / Wu, H. / Matthews, S.
History
DepositionApr 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
A: Fimbriae-associated protein Fap1
B: Fimbriae-associated protein Fap1
C: Fimbriae-associated protein Fap1
D: Fimbriae-associated protein Fap1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0015
Polymers57,8214
Non-polymers1801
Water724
1
A: Fimbriae-associated protein Fap1


Theoretical massNumber of molelcules
Total (without water)14,4551
Polymers14,4551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fimbriae-associated protein Fap1


Theoretical massNumber of molelcules
Total (without water)14,4551
Polymers14,4551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fimbriae-associated protein Fap1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6352
Polymers14,4551
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fimbriae-associated protein Fap1


Theoretical massNumber of molelcules
Total (without water)14,4551
Polymers14,4551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.885, 121.885, 117.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Fimbriae-associated protein Fap1


Mass: 14455.194 Da / Num. of mol.: 4
Fragment: The alpha subdomain of the major non-repeat unit of Fap1 fimbriae, residues 184-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus parasanguinis (bacteria) / Strain: FW213 / Gene: fap1 / Plasmid: PRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9ZFF9, UniProt: A1C3L3*PLUS
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.79 Å3/Da / Density % sol: 67.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.9 M Na/K phosphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.939 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 3→37.43 Å / Num. obs: 17284 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 102.925 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
3-3.164.40.3932.82502195.9
9.49-37.433.80.04918.5527181.2

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0104refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2kub

2kub


Resolution: 3→37.43 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.49 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24194 885 5.1 %RANDOM
Rwork0.22292 ---
obs0.22387 16333 93.72 %-
all-16333 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 3→37.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 12 4 2554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222599
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9993534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9675346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49428.333108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.75315472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.263157
X-RAY DIFFRACTIONr_chiral_restr0.0990.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211871
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 65 -
Rwork0.369 1078 -
obs--94.31 %

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