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- PDB-7f7y: Crystal Structure of protein PitB from pilus islet-2 of Streptoco... -

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Basic information

Entry
Database: PDB / ID: 7f7y
TitleCrystal Structure of protein PitB from pilus islet-2 of Streptococcus pneumoniae
ComponentsPitB
KeywordsCELL ADHESION / backbone pilin / adhesin / PitB / PI-2 pilus / Streptococcus pneumoniae / isopeptide / CnaB fold
Function / homologyStreptococcal pilin isopeptide linker superfamily / Domain of unknown function DUF5979 / Domain of unknown function (DUF5979) / membrane / IODIDE ION / : / PitB
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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
DepositionJun 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Oct 26, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
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 / _citation_author.identifier_ORCID
Revision 1.3Nov 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: PitB
B: PitB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,02316
Polymers72,5722
Non-polymers1,45214
Water9,260514
1
A: PitB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2399
Polymers36,2861
Non-polymers9548
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-14 kcal/mol
Surface area16680 Å2
MethodPISA
2
B: PitB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7847
Polymers36,2861
Non-polymers4986
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.490, 82.659, 362.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2524-

HOH

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Components

#1: Protein PitB


Mass: 36285.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: pitB / Production host: Escherichia coli (E. coli) / References: UniProt: B3FNT1
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.73 Å3/Da / Density % sol: 66.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG4000, Lithium sulphate, Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.979235 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979235 Å / Relative weight: 1
ReflectionResolution: 2.128→54.983 Å / Num. obs: 52716 / % possible obs: 97.5 % / Redundancy: 3.8 % / CC1/2: 0.994 / Net I/σ(I): 6.6
Reflection shellResolution: 2.128→2.24 Å / Redundancy: 3.8 % / Num. unique obs: 8511 / CC1/2: 0.902 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S3L

4s3l


Resolution: 2.13→54.98 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.877 / SU B: 8.414 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23541 2521 4.9 %RANDOM
Rwork0.19827 ---
obs0.20011 48546 81.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.942 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.13→54.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5106 0 22 514 5642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0135208
X-RAY DIFFRACTIONr_bond_other_d0.0180.0174814
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.667064
X-RAY DIFFRACTIONr_angle_other_deg1.6731.58911164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3175662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.15426.033242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47715890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.548158
X-RAY DIFFRACTIONr_chiral_restr0.090.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025974
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021090
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
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_it1.6681.3682654
X-RAY DIFFRACTIONr_mcbond_other1.6681.3672653
X-RAY DIFFRACTIONr_mcangle_it2.7982.043314
X-RAY DIFFRACTIONr_mcangle_other2.7972.0413315
X-RAY DIFFRACTIONr_scbond_it2.1451.5792554
X-RAY DIFFRACTIONr_scbond_other2.1451.5772552
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6022.2543750
X-RAY DIFFRACTIONr_long_range_B_refined7.00245.98783834
X-RAY DIFFRACTIONr_long_range_B_other6.9946.0583503
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.13→2.183 Å
RfactorNum. reflection% reflection
Rfree0.268 123 -
Rwork0.243 2560 -
obs--59.27 %
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)
10.0048-0.00680.030.02-0.06380.327-0-0.00040.0023-0.00210.01410.00570.02350.0098-0.01410.02210.0038-0.00380.02690.0050.0121-11.1258-13.28971.1225
20.00140.0059-0.00470.03510.01160.24560.0034-0.00020.0002-0.0010.01110.00510.00790.0057-0.01450.0127-0.0139-0.0060.0317-0.00240.0144-17.1183-11.3073-40.4273
30.0306-0.01190.09780.0072-0.04280.38980.0138-0.0064-0.0041-0.00040.0019-0.0032-0.0073-0.0297-0.01570.03120.0018-0.0020.0150.00720.0129-50.0609-13.5995-91.6096
40.00910.0128-0.05350.0186-0.07420.32130.00370.0024-0.00020.0030.0029-0.002-0.0153-0.0233-0.00660.0356-0.0155-0.00340.01390.00820.0088-47.1153-20.6869-50.1864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 222
2X-RAY DIFFRACTION2A223 - 379
3X-RAY DIFFRACTION3B48 - 222
4X-RAY DIFFRACTION4B223 - 379

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