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- PDB-7w6b: Crystal Structure of PitA from pilus islet-2 of Streptococcus oralis -

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Basic information

Entry
Database: PDB / ID: 7w6b
TitleCrystal Structure of PitA from pilus islet-2 of Streptococcus oralis
Componentsvon Willebrand factor type A domain protein
KeywordsCELL ADHESION / Tip pilin / adhesin / PitA / PI-2 pilus / Streptococcus oralis / isopeptide / CnaA fold / CnaB fold / vWFA fold / dental plaque / biofilm
Function / homologyDomain of unknown function DUF5979 / Domain of unknown function (DUF5979) / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / membrane / IODIDE ION / von Willebrand factor type A domain protein
Function and homology information
Biological speciesStreptococcus oralis ATCC 35037 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.984 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
DepositionDec 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Derived calculations / Category: atom_type / citation
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,06218
Polymers88,0941
Non-polymers1,96817
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area39410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.271, 422.928, 48.391
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 88094.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus oralis ATCC 35037 (bacteria)
Gene: HMPREF8579_1184 / Production host: Escherichia coli (E. coli) / References: UniProt: D4FSQ3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.04 Å3/Da / Density % sol: 59.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 100 mM HEPES pH 7.8, 1 M potassium iodide, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.7712 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.984→51.93 Å / Num. obs: 20771 / % possible obs: 95 % / Redundancy: 7 % / CC1/2: 0.991 / Rpim(I) all: 0.072 / Net I/σ(I): 10.6
Reflection shellResolution: 2.984→3.068 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1039 / CC1/2: 0.577 / Rpim(I) all: 0.479

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VCR

7vcr


Resolution: 2.984→51.93 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.807 / WRfactor Rfree: 0.284 / WRfactor Rwork: 0.242 / SU B: 39.76 / SU ML: 0.391 / Average fsc free: 0 / Average fsc work: 0 / Cross valid method: FREE R-VALUE / ESU R Free: 0.526 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.3052 1068 5.142 %
Rwork0.2533 19703 -
all0.256 --
obs-20771 90.125 %
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: 85.705 Å2
Baniso -1Baniso -2Baniso -3
1-2.478 Å2-0 Å20 Å2
2---0.729 Å20 Å2
3----1.749 Å2
Refinement stepCycle: LAST / Resolution: 2.984→51.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5878 0 17 31 5926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125977
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.6448120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5535781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56724.441295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.75315966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.791525
X-RAY DIFFRACTIONr_chiral_restr0.1050.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024573
X-RAY DIFFRACTIONr_nbd_refined0.2220.22007
X-RAY DIFFRACTIONr_nbtor_refined0.310.23988
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2139
X-RAY DIFFRACTIONr_metal_ion_refined0.2970.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3730.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0950.22
X-RAY DIFFRACTIONr_mcbond_it4.0417.8753127
X-RAY DIFFRACTIONr_mcangle_it6.93111.8093907
X-RAY DIFFRACTIONr_scbond_it3.9817.4382850
X-RAY DIFFRACTIONr_scangle_it6.74411.194213
X-RAY DIFFRACTIONr_lrange_it15.007145.65324081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.984-3.0610.37570.348887X-RAY DIFFRACTION56.4593
3.061-3.1450.403610.349972X-RAY DIFFRACTION64.9277
3.145-3.2360.349810.2931119X-RAY DIFFRACTION73.5745
3.236-3.3360.277510.2461108X-RAY DIFFRACTION78.3638
3.336-3.4450.281660.2421286X-RAY DIFFRACTION88.6557
3.445-3.5660.302640.2441353X-RAY DIFFRACTION99.0909
3.566-3.7010.3670.2571336X-RAY DIFFRACTION99.6449
3.701-3.8520.351600.2491256X-RAY DIFFRACTION100
3.852-4.0230.325640.251284X-RAY DIFFRACTION99.9259
4.023-4.2190.274810.2521131X-RAY DIFFRACTION100
4.219-4.4470.284610.2321160X-RAY DIFFRACTION99.8365
4.447-4.7170.227540.2061050X-RAY DIFFRACTION100
4.717-5.0420.261360.2211013X-RAY DIFFRACTION99.9048
5.042-5.4460.28660.237954X-RAY DIFFRACTION99.9021
5.446-5.9660.316470.284877X-RAY DIFFRACTION100
5.966-6.6690.55330.318806X-RAY DIFFRACTION100
6.669-7.6990.409510.298703X-RAY DIFFRACTION99.4723
7.699-9.4270.245370.231605X-RAY DIFFRACTION98.9214
9.427-13.3180.261250.206502X-RAY DIFFRACTION97.9554
13.318-51.930.31560.316301X-RAY DIFFRACTION93.8838
Refinement TLS params.Method: refined / Origin x: -11.7668 Å / Origin y: 68.6396 Å / Origin z: -1.9585 Å
111213212223313233
T0.0517 Å20.0196 Å2-0.0436 Å2-0.0432 Å20.0149 Å2--0.1816 Å2
L0.0652 °20.1138 °20.0415 °2-0.5496 °20.4045 °2--0.3904 °2
S-0.0517 Å °-0.0326 Å °0.0065 Å °-0.0905 Å °0.0172 Å °0.1273 Å °-0.0093 Å °0.0464 Å °0.0345 Å °
Refinement TLS groupSelection: ALL

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