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- PDB-3zpp: Structure of the Streptococcus pneumoniae surface protein and adh... -

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Basic information

Entry
Database: PDB / ID: 3zpp
TitleStructure of the Streptococcus pneumoniae surface protein and adhesin PfbA
ComponentsCELL WALL SURFACE ANCHOR FAMILY PROTEIN
KeywordsCELL ADHESION / PFBA / SURFACE ADHESIN / SP1833 / MSCRAMM
Function / homology
Function and homology information


cell wall / extracellular region / membrane / metal ion binding
Similarity search - Function
Right handed beta helix domain / Right handed beta helix region / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / YSIRK type signal peptide / Pectin lyase fold ...Right handed beta helix domain / Right handed beta helix region / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / YSIRK type signal peptide / Pectin lyase fold / YSIRK Gram-positive signal peptide / Pectin lyase fold/virulence factor / 3 Solenoid / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Mainly Beta
Similarity search - Domain/homology
Cell wall surface anchor family protein / Cell wall surface anchor family protein
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsL Suits, M.D. / Boraston, A.B.
CitationJournal: Plos One / Year: 2013
Title: Structure of the Streptococcus Pneumoniae Surface Protein and Adhesin Pfba.
Authors: Suits, M.D. / Boraston, A.B.
History
DepositionFeb 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELL WALL SURFACE ANCHOR FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4442
Polymers48,4041
Non-polymers401
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.840, 140.650, 128.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CELL WALL SURFACE ANCHOR FAMILY PROTEIN / SP_1833


Mass: 48404.105 Da / Num. of mol.: 1 / Fragment: CORE-DOMAIN, RESIDUES 139-560
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97P11, UniProt: A0A0H2URN9*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS IS A TRUNCATED FORM OF THE PROTEIN SPANNING RESIDUES 139-560.

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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: 2.94 Å3/Da / Density % sol: 58 %
Description: STRUCTURE WAS SOLVED VIA MR FROM A SAD SELENOMETHIONINE DERIVATIVE.
Crystal growpH: 5.5
Details: 12% (W/V) 10K POLYETHYLENE GLYCOL, 80 MM MG DIFORMATE (C2H2MGO4) AND BIS-TRIS-HCL (PH 5.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2012 / Details: VERTICAL COLLIMATING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.28→38 Å / Num. obs: 26446 / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.7
Reflection shellResolution: 2.28→2.4 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→57.44 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.253 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY N-TERMINAL IMAC AFFINITY TAG IS PRESENT IN THE CONSTRUCT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY N-TERMINAL IMAC AFFINITY TAG IS PRESENT IN THE CONSTRUCT BUT NOT MODELED INTO THE COORDINATES DUE TO THE ABSENCE OF CLEAR ELECTRON DENSITY FOR THIS REGION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 1340 5.1 %RANDOM
Rwork0.20804 ---
obs0.21045 25097 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.156 Å2
Baniso -1Baniso -2Baniso -3
1-5.26 Å20 Å20 Å2
2--1.04 Å20 Å2
3----6.29 Å2
Refinement stepCycle: LAST / Resolution: 2.28→57.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 1 59 3296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193311
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9484481
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.795428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.60326.346156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.50515587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.727158
X-RAY DIFFRACTIONr_chiral_restr0.1190.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022501
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 85 -
Rwork0.306 1859 -
obs--100 %

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