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- PDB-2x12: pH-induced modulation of Streptococcus parasanguinis adhesion by ... -

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Basic information

Entry
Database: PDB / ID: 2x12
TitlepH-induced modulation of Streptococcus parasanguinis adhesion by Fap1 fimbriae
ComponentsFIMBRIAE-ASSOCIATED PROTEIN FAP1
KeywordsCELL ADHESION / BIOFILM / CELL WALL / PEPTIDOGLYCAN-ANCHOR
Function / homology
Function and homology information


pilus / cell adhesion / extracellular region / cytoplasm
Similarity search - Function
Immunoglobulin-like - #2010 / Protein of unknown function DUF445 / : / Protein of unknown function (DUF445) / Serine-rich repeat adhesion glycoprotein / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain ...Immunoglobulin-like - #2010 / Protein of unknown function DUF445 / : / Protein of unknown function (DUF445) / Serine-rich repeat adhesion glycoprotein / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fap1 adhesin / Fap1 adhesin
Similarity search - Component
Biological speciesSTREPTOCOCCUS PARASANGUINIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsRamboarina, S. / Murray, J.W. / Garnett, J. / Matthews, S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural Insights Into Serine-Rich Fimbriae from Gram-Positive Bacteria.
Authors: Ramboarina, S. / Garnett, J.A. / Zhou, M. / Li, Y. / Peng, Z. / Taylor, J.D. / Lee, W.-C. / Bodey, A. / Murray, J.W. / Alguel, Y. / Bergeron, J. / Bardiaux, B. / Sawyer, E. / Isaacson, R. / ...Authors: Ramboarina, S. / Garnett, J.A. / Zhou, M. / Li, Y. / Peng, Z. / Taylor, J.D. / Lee, W.-C. / Bodey, A. / Murray, J.W. / Alguel, Y. / Bergeron, J. / Bardiaux, B. / Sawyer, E. / Isaacson, R. / Tagliaferri, C. / Cota, E. / Nilges, M. / Simpson, P. / Ruiz, T. / Wu, H. / Matthews, S.
History
DepositionDec 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIMBRIAE-ASSOCIATED PROTEIN FAP1
B: FIMBRIAE-ASSOCIATED PROTEIN FAP1


Theoretical massNumber of molelcules
Total (without water)74,5282
Polymers74,5282
Non-polymers00
Water00
1
A: FIMBRIAE-ASSOCIATED PROTEIN FAP1


Theoretical massNumber of molelcules
Total (without water)37,2641
Polymers37,2641
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FIMBRIAE-ASSOCIATED PROTEIN FAP1


Theoretical massNumber of molelcules
Total (without water)37,2641
Polymers37,2641
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.668, 108.668, 126.252
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A253 - 452
2111B253 - 452

NCS oper: (Code: given
Matrix: (0.9818, 0.1886, -0.02117), (0.1885, -0.9821, -0.00381), (-0.02151, -0.00025, -0.9998)
Vector: -6.824, 72.61, 6.229)

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Components

#1: Protein FIMBRIAE-ASSOCIATED PROTEIN FAP1 / FAP1


Mass: 37264.195 Da / Num. of mol.: 2 / Fragment: BETA DOMAIN, RESIDUES 174-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PARASANGUINIS (bacteria) / Strain: FW213 / Plasmid: PRSETA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q9ZFF9, UniProt: A1C3L3*PLUS
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: 5.1 Å3/Da / Density % sol: 76 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: 0.1 M HEPES PH 8.0, 11% (W/V) PEG 6K, 10 MM SPERMINE-TETRA HCL HANGING DROP VAPOUR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.9→47.04 Å / Num. obs: 19567 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.58 % / Biso Wilson estimate: 65.6 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.19
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 7.88 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.61 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0104refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.9→38.405 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.888 / SU B: 26.334 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.42 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 1003 5.12 %RANDOM
Rwork0.211 ---
obs0.213 19543 99.821 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.212 Å2
Baniso -1Baniso -2Baniso -3
1-3.895 Å21.948 Å2-0 Å2
2--3.895 Å2-0 Å2
3----5.843 Å2
Refinement stepCycle: LAST / Resolution: 2.9→38.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2988 0 0 0 2988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223052
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.9454162
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1145398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.0225.5120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.29615462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.228154
X-RAY DIFFRACTIONr_chiral_restr0.0870.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213458
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.2549
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2030.21601
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0040.21
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1580.25
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5721.51972
X-RAY DIFFRACTIONr_mcbond_other0.1131.5824
X-RAY DIFFRACTIONr_mcangle_it1.12823184
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.82231080
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1574.5978
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2462 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.050.05
2Btight positional0.050.05
1Atight thermal0.090.5
2Btight thermal0.090.5
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 81 -
Rwork0.348 1343 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4641-0.6526-1.0474.20970.57438.69710.027-0.00130.2693-0.3180.0279-0.0545-0.70730.5759-0.05490.2485-0.1546-0.00370.22850.07520.1078-43.631323.3093-1.0811
21.5413-0.2993-1.04762.0449-0.85716.8444-0.1240.1430.1033-0.28430.1128-0.19170.11420.66650.01120.1298-0.02890.03470.2282-0.00410.1238-40.227712.22736.0187
32.0566-0.44760.353.748-1.77448.2206-0.01320.07040.0611-0.39570.01820.2709-0.3992-0.2994-0.00510.1883-0.08230.01530.1834-0.01450.1084-49.153718.71911.9589
42.18451.0252-0.30783.63440.2756.98490.0615-0.2062-0.12010.2849-0.1871-0.06580.4426-0.05860.12560.22320.0490.04880.19290.04670.1098-44.787541.69127.024
52.17570.1505-0.36812.1011-0.546511.13280.2508-0.11220.07070.3567-0.03810.3074-0.9447-0.2355-0.21270.26270.05170.05990.1077-0.02850.1523-46.205854.45010.9546
62.78450.7468-0.60383.2919-0.75049.1560.047-0.13430.09160.3244-0.04170.2660.256-0.6034-0.00530.16360.05530.06830.2084-0.06660.1065-48.834446.44034.8758
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A236 - 284
2X-RAY DIFFRACTION2A285 - 367
3X-RAY DIFFRACTION3A368 - 435
4X-RAY DIFFRACTION4B236 - 289
5X-RAY DIFFRACTION5B290 - 347
6X-RAY DIFFRACTION6B348 - 435

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