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- PDB-6pon: CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF FIBRONECTIN- BINDIN... -

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Basic information

Entry
Database: PDB / ID: 6pon
TitleCRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF FIBRONECTIN- BINDING PROTEIN PAVA FROM STREPTOCOCCUS PNEUMONIAE
ComponentsAdherence and virulence protein A
KeywordsCELL ADHESION / fibronectin-binding protein / Pneumococcal adherence and virulence factor A / PavA
Function / homology
Function and homology information


RQC complex / ribosomal large subunit binding / rescue of stalled ribosome / tRNA binding / cell surface / cytoplasm
Similarity search - Function
Rqc2 homolog RqcH, bacterial / NFACT, RNA-binding domain / NFACT protein RNA binding domain
Similarity search - Domain/homology
Rqc2 homolog RqcH / Rqc2 homolog RqcH
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.395 Å
AuthorsManne, K. / Narayana, S.V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01- AI106808 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structure of the N-terminal domain of the fibronectin-binding protein PavA from Streptococcus pneumoniae.
Authors: Manne, K. / Narayana, S.V.L. / Chattopadhyay, D.
History
DepositionJul 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Structure summary
Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adherence and virulence protein A
B: Adherence and virulence protein A


Theoretical massNumber of molelcules
Total (without water)62,8972
Polymers62,8972
Non-polymers00
Water6,612367
1
A: Adherence and virulence protein A

B: Adherence and virulence protein A


Theoretical massNumber of molelcules
Total (without water)62,8972
Polymers62,8972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_456x-1,y,z+11
Buried area5830 Å2
ΔGint-46 kcal/mol
Surface area26490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.873, 46.814, 83.678
Angle α, β, γ (deg.)90.000, 90.931, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Adherence and virulence protein A


Mass: 31448.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: pavA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RNF3, UniProt: Q8DQ36*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 27% (w/v) PEG 4000, 0.2 M Ammonium Acetate, 0.1 M Sodium Citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 4, 2018
RadiationMonochromator: Cu filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.395→83.667 Å / Num. obs: 23361 / % possible obs: 99 % / Redundancy: 3.26 % / Biso Wilson estimate: 25.5368070055 Å2 / Rpim(I) all: 0.06 / Rrim(I) all: 0.11 / Net I/σ(I): 7.1
Reflection shellResolution: 2.395→2.44 Å / Num. unique obs: 2228 / CC1/2: 0.841 / Rpim(I) all: 0.272

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H3X

5h3x


Resolution: 2.395→41.83 Å / SU ML: 0.266668916687 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.321888896
RfactorNum. reflection% reflection
Rfree0.237 1141 4.8846269104 %
Rwork0.1665 --
obs0.17 23359 99.2732681683 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.5245750125 Å2
Refinement stepCycle: LAST / Resolution: 2.395→41.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4188 0 0 368 4556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00809653728654266
X-RAY DIFFRACTIONf_angle_d0.9048340612695769
X-RAY DIFFRACTIONf_chiral_restr0.0522595940258665
X-RAY DIFFRACTIONf_plane_restr0.00499847624697750
X-RAY DIFFRACTIONf_dihedral_angle_d15.61663876292604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.395-2.5041592621X-RAY DIFFRACTION95.8620689655
2.504-2.6361502759X-RAY DIFFRACTION99.6915695682
2.636-2.80111342793X-RAY DIFFRACTION99.6934604905
2.8011-3.01741382754X-RAY DIFFRACTION99.7585374267
3.0174-3.32090.2532459912481640.1739475132422781X-RAY DIFFRACTION99.8305084746
3.3209-3.80120.2403303691751290.1508795050952793X-RAY DIFFRACTION99.9316005472
3.8012-4.7880.1940025943471380.1344106975072805X-RAY DIFFRACTION99.7965412004
4.788-41.83347673550.1792035307441290.1623686116952912X-RAY DIFFRACTION99.5743287492

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