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- PDB-4mr0: Crystal structure of PfbA, a surface adhesin of Streptococcus pne... -

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Basic information

Entry
Database: PDB / ID: 4mr0
TitleCrystal structure of PfbA, a surface adhesin of Streptococcus pneumoniae
ComponentsPlasmin and fibronectin-binding protein A
KeywordsPLASIMIN AND FIBRONECTIN-BINDING PROTEIN / Surface protein / Adhesion / Fibronectin / Plasminogen / CELL ADHESION
Function / homology
Function and homology information


cell wall / : / extracellular region / membrane
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 / Gram-positive cocci surface proteins LPxTG motif profile. / 3 Solenoid / LPXTG cell wall anchor domain / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / : / Plasmin and fibronectin-binding protein A
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsPonnuraj, K. / Beulin, D.S.J.
CitationJournal: Int.J.Biol.Macromol. / Year: 2013
Title: Crystal structure of PfbA, a surface adhesin of Streptococcus pneumoniae, provides hints into its interaction with fibronectin
Authors: Beulin, D.S.J. / Yamaguchi, M. / Kawabata, S. / Ponnuraj, K.
History
DepositionSep 17, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Data collection
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_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_asym_id / _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_asym_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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Plasmin and fibronectin-binding protein A
B: Plasmin and fibronectin-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,47016
Polymers142,7232
Non-polymers74714
Water10,233568
1
A: Plasmin and fibronectin-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7358
Polymers71,3621
Non-polymers3737
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Plasmin and fibronectin-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7358
Polymers71,3621
Non-polymers3737
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.590, 126.080, 63.480
Angle α, β, γ (deg.)90.00, 99.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Plasmin and fibronectin-binding protein A


Mass: 71361.703 Da / Num. of mol.: 2 / Fragment: UNP residues 150-607
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-255 / R6 / Gene: pfbA, spr1652 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q8CYC9

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Non-polymers , 5 types, 582 molecules

#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 1.68 Å3/Da / Density % sol: 26.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30-35% PEG3350, 0.1M Sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.97927, 0.97942, 0.95373
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 25, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979271
20.979421
30.953731
ReflectionResolution: 1.85→37.86 Å / Num. all: 145890 / Num. obs: 132827 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID
1.85-21
6.01-37.861

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Processing

Software
NameClassification
Auto-Rickshawphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.95→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2223 4039 RANDOM
Rwork0.2043 --
obs0.22 132827 -
all-145890 -
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6930 0 20 568 7518
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONBond lengths0.005
X-RAY DIFFRACTIONBond angles1.486

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