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- PDB-3qc6: GspB -

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Basic information

Entry
Database: PDB / ID: 3qc6
TitleGspB
ComponentsPlatelet binding protein GspB
KeywordsSUGAR BINDING PROTEIN / Carbohydrate/Sugar Binding
Function / homology
Function and homology information


cell adhesion / extracellular region
Similarity search - Function
Immunoglobulin-like - #3260 / Immunoglobulin-like - #4140 / 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. ...Immunoglobulin-like - #3260 / Immunoglobulin-like - #4140 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NITROGEN MOLECULE / Platelet binding protein GspB
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPyburn, T.M.
CitationJournal: Plos Pathog. / Year: 2011
Title: A Structural Model for Binding of the Serine-Rich Repeat Adhesin GspB to Host Carbohydrate Receptors.
Authors: Pyburn, T.M. / Bensing, B.A. / Xiong, Y.Q. / Melancon, B.J. / Tomasiak, T.M. / Ward, N.J. / Yankovskaya, V. / Oliver, K.M. / Cecchini, G. / Sulikowski, G.A. / Tyska, M.J. / Sullam, P.M. / Iverson, T.M.
History
DepositionJan 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Data collection
Revision 1.2Feb 21, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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
X: Platelet binding protein GspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7776
Polymers39,4971
Non-polymers2805
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.338, 86.743, 117.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Platelet binding protein GspB


Mass: 39496.672 Da / Num. of mol.: 1 / Fragment: unp residues 245-604 / Mutation: N444S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Plasmid: pGEX-3X / Production host: Escherichia coli (E. coli) / References: UniProt: Q939N5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-HDZ / NITROGEN MOLECULE / Nitrogen


Mass: 28.013 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE BOND DISTANCE BETWEEN N6A AND N6B ATOMS OF THE HDZ LIGAND IS NOT CONFORM TO THE STANDARD BOND ...THE BOND DISTANCE BETWEEN N6A AND N6B ATOMS OF THE HDZ LIGAND IS NOT CONFORM TO THE STANDARD BOND DISTANCE FOR HDZ

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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: 2.16 Å3/Da / Density % sol: 43.02 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mg/mL protein buffered in 20mM HEPES pH 7.5 equilibrated against a reservoir solution containing 25% PEG3350, 0.1M HEPES pH 7.5, 0.15M NH4CH3COO, and 10mM Spermidine, VAPOR DIFFUSION, ...Details: 10 mg/mL protein buffered in 20mM HEPES pH 7.5 equilibrated against a reservoir solution containing 25% PEG3350, 0.1M HEPES pH 7.5, 0.15M NH4CH3COO, and 10mM Spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.03034 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03034 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 26193 / % possible obs: 93.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.068
Reflection shellResolution: 1.9→1.97 Å / % possible all: 92.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→35.81 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.89 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 8.951 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 1265 4.8 %RANDOM
Rwork0.2153 ---
obs0.2174 26142 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 60.13 Å2 / Biso mean: 25.903 Å2 / Biso min: 11.85 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2721 0 17 225 2963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222806
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.943823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32925.113133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29315476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1471519
X-RAY DIFFRACTIONr_chiral_restr0.0870.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212109
X-RAY DIFFRACTIONr_mcbond_it0.7051.51753
X-RAY DIFFRACTIONr_mcangle_it1.2322869
X-RAY DIFFRACTIONr_scbond_it2.07831053
X-RAY DIFFRACTIONr_scangle_it3.3064.5949
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 84 -
Rwork0.25 1801 -
all-1885 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 1.4324 Å / Origin y: 9.2274 Å / Origin z: -5.1384 Å
111213212223313233
T0.0243 Å2-0.0058 Å20.0094 Å2-0.0343 Å2-0.0022 Å2--0.0107 Å2
L0.0376 °20.1132 °2-0.0543 °2-0.8044 °2-0.5156 °2--0.3688 °2
S-0.0257 Å °0.017 Å °-0.0071 Å °-0.0476 Å °0.0149 Å °-0.0359 Å °0.0383 Å °-0.0081 Å °0.0108 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X246 - 601
3X-RAY DIFFRACTION1X246 - 601

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