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

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Basic information

Entry
Database: PDB / ID: 7vcr
TitleCrystal Structure of PitA fragment from pilus islet-2 of Streptococcus oralis
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 / 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 / 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 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 1.0Jun 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
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


Theoretical massNumber of molelcules
Total (without water)110,0444
Polymers110,0444
Non-polymers00
Water6,918384
1
C: von Willebrand factor type A domain protein
A: von Willebrand factor type A domain protein


Theoretical massNumber of molelcules
Total (without water)55,0222
Polymers55,0222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-10 kcal/mol
Surface area25980 Å2
MethodPISA
2
D: von Willebrand factor type A domain protein
B: von Willebrand factor type A domain protein


Theoretical massNumber of molelcules
Total (without water)55,0222
Polymers55,0222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-9 kcal/mol
Surface area25510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.480, 70.875, 82.466
Angle α, β, γ (deg.)80.087, 87.024, 87.700
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
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: 51645.129 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 3.22 Å3/Da / Density % sol: 61.79 %
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: ID30B / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2→81.15 Å / Num. obs: 83573 / % possible obs: 90.3 % / Redundancy: 3.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.047 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.04 Å / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4541 / CC1/2: 0.727 / Rpim(I) all: 0.647 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VCN

7vcn


Resolution: 2→69.879 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 11.006 / SU ML: 0.135 / Cross valid method: FREE R-VALUE / ESU R: 0.173 / ESU R Free: 0.156 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2339 4294 5.139 %
Rwork0.2009 79271 -
all0.203 --
obs-83565 90.314 %
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: 57.196 Å2
Baniso -1Baniso -2Baniso -3
1-3.402 Å2-1.455 Å20.52 Å2
2---0.696 Å20.411 Å2
3----2.472 Å2
Refinement stepCycle: LAST / Resolution: 2→69.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7586 0 0 384 7970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0127711
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.65110426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0785965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.524.684380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.642151399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3421530
X-RAY DIFFRACTIONr_chiral_restr0.1390.21051
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025734
X-RAY DIFFRACTIONr_nbd_refined0.1960.22697
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25250
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2456
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.190.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.29
X-RAY DIFFRACTIONr_mcbond_it4.093.4083881
X-RAY DIFFRACTIONr_mcangle_it5.7665.0784839
X-RAY DIFFRACTIONr_scbond_it5.8473.9023830
X-RAY DIFFRACTIONr_scangle_it8.5535.5845587
X-RAY DIFFRACTIONr_lrange_it11.07664.92131030
X-RAY DIFFRACTIONr_ncsr_local_group_10.0840.0514655
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.083950.05008
12BX-RAY DIFFRACTIONLocal ncs0.083950.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.3343550.3265966X-RAY DIFFRACTION92.3313
2.052-2.1080.3183160.3065812X-RAY DIFFRACTION91.7228
2.108-2.1690.3043320.2795616X-RAY DIFFRACTION91.7901
2.169-2.2360.3212840.2645429X-RAY DIFFRACTION90.4242
2.236-2.3090.2942710.2655147X-RAY DIFFRACTION88.9655
2.309-2.390.3242380.264760X-RAY DIFFRACTION84.8125
2.39-2.480.2712630.2444931X-RAY DIFFRACTION90.6457
2.48-2.5810.2712290.2164878X-RAY DIFFRACTION92.939
2.581-2.6960.2532340.2044594X-RAY DIFFRACTION92.3312
2.696-2.8280.2552350.2014354X-RAY DIFFRACTION91.2507
2.828-2.980.2762000.24036X-RAY DIFFRACTION89.0852
2.98-3.1610.2532180.2123587X-RAY DIFFRACTION83.7
3.161-3.3790.2452170.2123775X-RAY DIFFRACTION94.0179
3.379-3.6490.2461900.2173461X-RAY DIFFRACTION92.571
3.649-3.9960.2291580.1933146X-RAY DIFFRACTION90.2732
3.996-4.4670.1831580.1462671X-RAY DIFFRACTION86.145
4.467-5.1550.161460.1262439X-RAY DIFFRACTION88.8927
5.155-6.3070.1971340.1612149X-RAY DIFFRACTION93.2979
6.307-8.8930.173740.1821569X-RAY DIFFRACTION86.4282
8.893-69.8790.198420.19951X-RAY DIFFRACTION95.0239
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)
10.62980.5924-0.19961.15260.59721.0991-0.1817-0.2756-0.1837-0.2455-0.0851-0.0119-0.0410.31470.26680.20660.03330.09280.22650.060.2204-18.343-20.856-45.354
20.08980.13220.16570.91271.46712.41190.039-0.0053-0.0806-0.037-0.0003-0.0541-0.1254-0.0556-0.03870.213-0.0868-0.04960.39130.02310.0792-21.9596-0.6606-25.2497
30.80960.1621-0.03441.0120.83270.81030.11970.1231-0.00730.03040.0032-0.14130.0009-0.1942-0.1230.193-0.0473-0.00790.35630.04120.1176-19.426212.92629.2529
40.0154-0.1314-0.12721.9020.76391.69990.01360.01680.00560.20970.06-0.2443-0.4229-0.4318-0.07360.33060.029-0.00590.38190.010.078-25.039531.760941.2808
50.1558-0.155-0.26940.73220.19550.49620.02450.00340.00840.05120.0337-0.0157-0.00720.0211-0.05820.2597-0.0338-0.01020.1843-0.05520.21211.9612.047-1.113
60.18180.10030.03740.93781.39072.17470.01960.02720.04940.0152-0.0039-0.02440.0893-0.072-0.01570.3128-0.04430.0160.1935-0.07090.14069.7058-11.6195-19.4064
70.39-0.0267-0.47290.81080.84041.42910.0724-0.07240.0075-0.0332-0.0495-0.037-0.0288-0.035-0.02290.3111-0.02540.00650.1792-0.07050.16269.9318-25.3947-53.9478
80.09080.0428-0.21231.818-0.60170.68730.02690.00740.0576-0.20670.0581-0.09230.0889-0.1118-0.0850.3322-0.05080.00140.1834-0.04650.13992.6362-45.1108-85.6454
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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