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- PDB-5eq4: Crystal structure of the SrpA adhesin R347E mutant from Streptoco... -

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Basic information

Entry
Database: PDB / ID: 5eq4
TitleCrystal structure of the SrpA adhesin R347E mutant from Streptococcus sanguinis
ComponentsPlatelet-binding glycoprotein
KeywordsSUGAR BINDING PROTEIN / bacterial adhesin / lectin / immunoglobulin fold / serine-rich repeat
Function / homology
Function and homology information


SrpA-like, SigLec-like domain / GspA/SrpA SigLec-like domain / Ubiquitin-like (UB roll) - #890 / Atypical Rib domain / Atypical Rib domain / Serine-rich repeat adhesion glycoprotein / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...SrpA-like, SigLec-like domain / GspA/SrpA SigLec-like domain / Ubiquitin-like (UB roll) - #890 / Atypical Rib domain / Atypical Rib domain / Serine-rich repeat adhesion glycoprotein / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Platelet-binding glycoprotein
Similarity search - Component
Biological speciesStreptococcus sanguinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsLoukachevitch, L.V. / McCulloch, K.M. / Vann, K.R. / Wawrzak, Z. / Anderson, S. / Iverson, T.M.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI106987 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI41513 United States
American Heart Association14GRNT 20390021 United States
Department of Veteran's Affairs United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008320 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)T32 HL007751 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR026915 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Michigan Economic Development Corporation085P1000817 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for Sialoglycan Binding by the Streptococcus sanguinis SrpA Adhesin.
Authors: Bensing, B.A. / Loukachevitch, L.V. / McCulloch, K.M. / Yu, H. / Vann, K.R. / Wawrzak, Z. / Anderson, S. / Chen, X. / Sullam, P.M. / Iverson, T.M.
History
DepositionNov 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 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
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.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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Platelet-binding glycoprotein
B: Platelet-binding glycoprotein
C: Platelet-binding glycoprotein
D: Platelet-binding glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,54815
Polymers88,0694
Non-polymers47911
Water11,998666
1
A: Platelet-binding glycoprotein
B: Platelet-binding glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3539
Polymers44,0352
Non-polymers3187
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-36 kcal/mol
Surface area19920 Å2
MethodPISA
2
C: Platelet-binding glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0973
Polymers22,0171
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-11 kcal/mol
Surface area10840 Å2
MethodPISA
3
D: Platelet-binding glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0973
Polymers22,0171
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.700, 88.055, 199.214
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Platelet-binding glycoprotein


Mass: 22017.254 Da / Num. of mol.: 4 / Mutation: R347E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sanguinis (bacteria) / Strain: SK36 / Gene: srpA, SSA_0829 / Plasmid: pGEX3X / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: A3CM52
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM Na cacodylate, 0.2 M NaCH3COO, 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 33121 / % possible obs: 91.8 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.045 / Rrim(I) all: 0.105 / Χ2: 1.685 / Net I/av σ(I): 14.19 / Net I/σ(I): 7.6 / Num. measured all: 157498
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.343.60.56312680.7590.3160.6510.8271.6
2.34-2.383.70.48114740.8180.2650.5540.81483.1
2.38-2.433.90.46515460.8140.2530.5340.81488
2.43-2.4840.35615720.90.1820.4030.8287.2
2.48-2.534.40.32415540.9120.1590.3630.81688.6
2.53-2.594.60.31116350.9310.1490.3470.87491.7
2.59-2.664.60.26116300.9440.1240.290.91392.4
2.66-2.734.70.23416760.9620.1120.2610.90594.6
2.73-2.814.60.19617220.970.0950.2190.91395
2.81-2.94.70.17116780.980.0820.1910.9396.1
2.9-34.70.14517480.9830.070.1621.04496
3-3.124.80.12117120.9880.0580.1351.06496.6
3.12-3.264.90.10117160.9890.0480.1131.44495.9
3.26-3.4450.0917520.9920.0420.11.7396.3
3.44-3.655.10.0817230.9940.0380.0891.36795.8
3.65-3.935.20.06717190.9930.0310.0741.63195.3
3.93-4.335.30.05717410.9950.0260.0631.56594.8
4.33-4.955.50.05317450.9960.0240.0592.48393.9
4.95-6.245.70.04717350.9970.020.0522.65493.1
6.24-505.30.04117750.9830.020.0467.10188.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.3 Å44.03 Å
Translation2.3 Å44.03 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→43.35 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 1652 5 %
Rwork0.2018 31389 -
obs0.2045 33041 91.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.97 Å2 / Biso mean: 31.0859 Å2 / Biso min: 8.09 Å2
Refinement stepCycle: final / Resolution: 2.3→43.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5935 0 17 666 6618
Biso mean--27.81 31.22 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076154
X-RAY DIFFRACTIONf_angle_d0.4578366
X-RAY DIFFRACTIONf_chiral_restr0.044980
X-RAY DIFFRACTIONf_plane_restr0.0041114
X-RAY DIFFRACTIONf_dihedral_angle_d10.0653715
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2982-2.36580.29151110.24742114222575
2.3658-2.44220.3221270.24012418254588
2.4422-2.52940.28181310.22892490262188
2.5294-2.63070.26451370.23092595273292
2.6307-2.75040.29741390.22952650278995
2.7504-2.89540.29751420.22882687282996
2.8954-3.07680.29031440.22332732287696
3.0768-3.31420.24991440.20862734287896
3.3142-3.64760.26361450.19572754289996
3.6476-4.17510.21161440.17992736288095
4.1751-5.25870.22361440.16312739288394
5.2587-43.35770.24041440.18462740288489

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