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- PDB-7vcn: Crystal Structure of PitA fragment from pilus islet-2 of Streptoc... -

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Basic information

Entry
Database: PDB / ID: 7vcn
TitleCrystal Structure of PitA fragment from pilus islet-2 of Streptococcus oralis with Tb-Xo4
Components(von Willebrand factor type A domain protein) x 2
KeywordsCELL ADHESION / Tip pilin / adhesin / PitA / PI-2 pilus / Streptococcus oralis / isopeptide / CnaA fold / CnaB fold / Crystallophore / Terbium / biofilm / dental plaque
Function / homology
Function and homology information


Domain of unknown function DUF5979 / Domain of unknown function (DUF5979) / Collagen-binding surface protein Cna, B-type domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tb-Xo4 / TERBIUM(III) ION / von Willebrand factor type A domain protein
Similarity search - Component
Biological speciesStreptococcus oralis ATCC 35037 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.343 Å
AuthorsYadav, R.K. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2019/000432 India
CitationJournal: Febs J. / Year: 2022
Title: New structural insights into the PI-2 pilus from Streptococcus oralis, an early dental plaque colonizer.
Authors: Yadav, R.K. / Krishnan, V.
History
DepositionSep 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 2.0Aug 12, 2026Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / pdbx_entry_details ...chem_comp / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _chem_comp.formula / _pdbx_entry_details.has_protein_modification
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: von Willebrand factor type A domain protein
A: von Willebrand factor type A domain protein
D: von Willebrand factor type A domain protein
B: von Willebrand factor type A domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,6609
Polymers111,0714
Non-polymers1,5895
Water2,054114
1
C: von Willebrand factor type A domain protein
A: von Willebrand factor type A domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4105
Polymers55,5352
Non-polymers8743
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-13 kcal/mol
Surface area25980 Å2
MethodPISA
2
D: von Willebrand factor type A domain protein
B: von Willebrand factor type A domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2514
Polymers55,5352
Non-polymers7152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-15 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.815, 70.288, 82.710
Angle α, β, γ (deg.)79.883, 86.895, 87.186
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDAuth seq-ID
111A40 - 821
221B40 - 821

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Components

#1: Protein/peptide von Willebrand factor type A domain protein / PitA


Mass: 3376.763 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: residues 70-357 was removed during limited proteolysis treatment.
Source: (gene. exp.) Streptococcus oralis ATCC 35037 (bacteria)
Gene: HMPREF8579_1184 / Production host: Escherichia coli (E. coli) / References: UniProt: D4FSQ3
#2: Protein von Willebrand factor type A domain protein / PitA


Mass: 52158.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: residues 70-357 was removed during limited proteolysis treatment.
Source: (gene. exp.) Streptococcus oralis ATCC 35037 (bacteria)
Gene: HMPREF8579_1184 / Production host: Escherichia coli (E. coli) / References: UniProt: D4FSQ3
#3: Chemical ChemComp-7MT / Tb-Xo4


Mass: 556.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N5O4Tb
#4: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Tb
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.2 M ammonium acetate 0.1 M HEPES pH 7.2, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.42379 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.42379 Å / Relative weight: 1
ReflectionResolution: 2.343→69.235 Å / Num. obs: 38153 / % possible obs: 82.6 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.03 / Net I/σ(I): 15.7
Reflection shellResolution: 2.343→2.608 Å / Rmerge(I) obs: 0.552 / Num. unique obs: 1909 / CC1/2: 0.881 / Rpim(I) all: 0.252

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.343→69.139 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU B: 18.323 / SU ML: 0.196 / Cross valid method: FREE R-VALUE / ESU R: 0.639 / ESU R Free: 0.302 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2396 1787 4.684 %
Rwork0.1942 36366 -
all0.196 --
obs-38153 66.425 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 62.857 Å2
Baniso -1Baniso -2Baniso -3
1-0.747 Å2-0.162 Å2-1.082 Å2
2---0.291 Å20.637 Å2
3----0.327 Å2
Refinement stepCycle: LAST / Resolution: 2.343→69.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7581 0 63 114 7758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0127784
X-RAY DIFFRACTIONr_angle_refined_deg1.821.66510533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6475963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.61124.684380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.108151402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.951530
X-RAY DIFFRACTIONr_chiral_restr0.1210.21059
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025760
X-RAY DIFFRACTIONr_nbd_refined0.2110.22583
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25227
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2252
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2090.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.26
X-RAY DIFFRACTIONr_mcbond_it3.2263.2693873
X-RAY DIFFRACTIONr_mcangle_it5.3564.8834829
X-RAY DIFFRACTIONr_scbond_it4.2063.6223911
X-RAY DIFFRACTIONr_scangle_it6.6035.2675704
X-RAY DIFFRACTIONr_lrange_it10.85561.10930786
X-RAY DIFFRACTIONr_ncsr_local_group_10.130.0514045
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.130090.05007
12BX-RAY DIFFRACTIONLocal ncs0.130090.05007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.343-2.4040.38470.255203X-RAY DIFFRACTION4.9775
2.404-2.470.349280.303338X-RAY DIFFRACTION8.8278
2.47-2.5410.337290.308535X-RAY DIFFRACTION14.1071
2.541-2.620.385500.311888X-RAY DIFFRACTION23.9653
2.62-2.7050.359630.2821328X-RAY DIFFRACTION36.586
2.705-2.80.314980.2822002X-RAY DIFFRACTION56.8182
2.8-2.9060.3551250.2862903X-RAY DIFFRACTION86.7125
2.906-3.0240.3151480.263168X-RAY DIFFRACTION96.9591
3.024-3.1590.2741450.2423040X-RAY DIFFRACTION97.1333
3.159-3.3120.2981730.2272859X-RAY DIFFRACTION97.5233
3.312-3.4910.2781380.2152758X-RAY DIFFRACTION97.7388
3.491-3.7030.2451180.2152636X-RAY DIFFRACTION97.8678
3.703-3.9580.2561020.1982471X-RAY DIFFRACTION98.0564
3.958-4.2740.2221140.1672305X-RAY DIFFRACTION98.2934
4.274-4.6810.1621100.1342137X-RAY DIFFRACTION98.5526
4.681-5.2310.17960.121906X-RAY DIFFRACTION98.7179
5.231-6.0360.199860.1531704X-RAY DIFFRACTION99.1141
6.036-7.3820.216600.1621445X-RAY DIFFRACTION99.0132
7.382-10.3980.15660.1381123X-RAY DIFFRACTION99.4979
10.398-69.1390.195310.175617X-RAY DIFFRACTION99.2343
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)
10.69960.5629-0.08640.84640.37220.5129-0.1239-0.2682-0.2927-0.2556-0.1205-0.0826-0.14210.11640.24430.28150.08650.11520.30310.09590.3951-18.522-20.755-45.247
20.01380.03520.07411.33931.58052.5579-0.006-0.0255-0.0449-0.0397-0.06280.0233-0.1418-0.02980.06880.1771-0.06330.00230.56270.05150.2071-21.7014-0.7722-25.3065
30.61810.1164-0.26941.0851.05551.39260.07530.19890.04120.12330.0654-0.160.0886-0.2856-0.14060.2281-0.01550.040.51190.0260.2186-19.086312.88519.2544
40.01540.1242-0.0181.48340.19741.6340.02930.0485-0.04280.39840.118-0.4267-0.5267-0.718-0.14730.43890.2004-0.01890.56010.0050.1702-25.012131.439841.0992
50.1869-0.0028-0.2460.68710.30290.45980.0320.03050.02440.0790.0026-0.05710.0262-0.0225-0.03460.34280.01480.00640.2865-0.0290.33542.05512.153-1.187
60.15090.08580.00911.09221.45972.08550.02470.01430.05570.0435-0.0309-0.04660.1223-0.07760.00610.3708-0.01770.04030.2876-0.03270.29299.6419-11.0382-19.5048
70.3170.1177-0.07240.78250.8721.13770.0657-0.0320.04350.0095-0.0194-0.01370.0476-0.0436-0.04630.37250.03670.02910.2779-0.04220.30799.7786-24.956-54.0289
80.01740.1136-0.04081.8775-0.45711.267-0.0144-0.02840.0457-0.23410.0811-0.05490.2176-0.085-0.06680.3987-0.00890.01710.2836-0.04320.30571.9871-44.686-85.7095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLC40 - 69
2X-RAY DIFFRACTION1ALLB358 - 499
3X-RAY DIFFRACTION2ALLB500 - 604
4X-RAY DIFFRACTION3ALLB605 - 710
5X-RAY DIFFRACTION4ALLB711 - 821
6X-RAY DIFFRACTION5ALLD40 - 69
7X-RAY DIFFRACTION5ALLA358 - 499
8X-RAY DIFFRACTION6ALLA500 - 604
9X-RAY DIFFRACTION7ALLA605 - 710
10X-RAY DIFFRACTION8ALLA711 - 823

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