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- PDB-3qc5: GspB -

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Basic information

Entry
Database: PDB / ID: 3qc5
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 / molecular replacement / Resolution: 1.4 Å
AuthorsPyburn, T.M. / Iverson, 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 1.1Nov 8, 2017Group: Refinement description / Category: software
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_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_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_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)39,8637
Polymers39,4971
Non-polymers3666
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.681, 96.753, 100.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules X

#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) / Gene: gspB / Production host: Escherichia coli (E. coli) / References: UniProt: Q939N5

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Non-polymers , 5 types, 391 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-HDZ / NITROGEN MOLECULE


Mass: 28.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 296.15 K / pH: 7.4
Details: 6 mg/mL GspB buffered in 20 mM Tris, 33% Jeffamine ED-2001, 0.1 M HEPES, 0.15 M KCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 296.15K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 60816 / % possible obs: 92.7 % / Observed criterion σ(I): 2
Reflection shellResolution: 1.4→1.45 Å / % possible all: 54.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→30.7 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 1.91 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.172 2542 4.2 %RANDOM
Rwork0.142 ---
obs0.144 60741 99.6 %-
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 mean: 17.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 22 385 3132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222978
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9434108
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9015414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39925.455143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.84815513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3431519
X-RAY DIFFRACTIONr_chiral_restr0.0980.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212273
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_it1.4031.51845
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.24923063
X-RAY DIFFRACTIONr_scbond_it3.24831133
X-RAY DIFFRACTIONr_scangle_it5.0094.51011
X-RAY DIFFRACTIONr_rigid_bond_restr1.43532978
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 136 -
Rwork0.236 2313 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 23.3889 Å / Origin y: 66.9698 Å / Origin z: 36.9592 Å
111213212223313233
T0.0156 Å2-0.0069 Å20.0015 Å2-0.0089 Å20.0008 Å2--0.0289 Å2
L0.0527 °2-0.0107 °2-0.0233 °2-0.0289 °2-0.0983 °2--0.4904 °2
S0.0042 Å °-0.0086 Å °-0.004 Å °-0.0008 Å °0.0129 Å °0.0073 Å °-0.0365 Å °-0.0249 Å °-0.017 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X246 - 604
2X-RAY DIFFRACTION1X246 - 604

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