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- PDB-6efi: SK678 binding region (Siglec + Unique) -

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Basic information

Entry
Database: PDB / ID: 6efi
TitleSK678 binding region (Siglec + Unique)
ComponentsKxYKxGKxW signal domain protein
KeywordsSUGAR BINDING PROTEIN / lectin
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
: / KxYKxGKxW signal domain protein
Similarity search - Component
Biological speciesStreptococcus sanguinis SK678 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.715 Å
AuthorsIverson, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI106987 United States
CitationJournal: Nat Commun / Year: 2022
Title: Origins of glycan selectivity in streptococcal Siglec-like adhesins suggest mechanisms of receptor adaptation.
Authors: Bensing, B.A. / Stubbs, H.E. / Agarwal, R. / Yamakawa, I. / Luong, K. / Solakyildirim, K. / Yu, H. / Hadadianpour, A. / Castro, M.A. / Fialkowski, K.P. / Morrison, K.M. / Wawrzak, Z. / Chen, ...Authors: Bensing, B.A. / Stubbs, H.E. / Agarwal, R. / Yamakawa, I. / Luong, K. / Solakyildirim, K. / Yu, H. / Hadadianpour, A. / Castro, M.A. / Fialkowski, K.P. / Morrison, K.M. / Wawrzak, Z. / Chen, X. / Lebrilla, C.B. / Baudry, J. / Smith, J.C. / Sullam, P.M. / Iverson, T.M.
History
DepositionAug 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_symmetry
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KxYKxGKxW signal domain protein
B: KxYKxGKxW signal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,05426
Polymers46,3712
Non-polymers1,68324
Water9,242513
1
A: KxYKxGKxW signal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,93312
Polymers23,1861
Non-polymers74811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: KxYKxGKxW signal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,12114
Polymers23,1861
Non-polymers93513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.624, 59.579, 61.832
Angle α, β, γ (deg.)90.00, 100.74, 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 KxYKxGKxW signal domain protein


Mass: 23185.537 Da / Num. of mol.: 2 / Fragment: residues 251-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sanguinis SK678 (bacteria)
Gene: srpA, HMPREF9392_0959 / Production host: Escherichia coli (E. coli) / References: UniProt: F0FS71

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Non-polymers , 5 types, 537 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M bicine pH 7.6, 25% PEG 6000, 0.005 M hexamine Cobalt chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 45715 / % possible obs: 97.7 % / Redundancy: 7 % / Net I/σ(I): 15
Reflection shellResolution: 1.7→1.74 Å

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Processing

SoftwareName: PHENIX / Version: (1.12_2829) / Classification: refinement
RefinementResolution: 1.715→38.718 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2117 1991 4.64 %
Rwork0.1807 --
obs0.1822 42886 93.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.715→38.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3145 0 103 513 3761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083301
X-RAY DIFFRACTIONf_angle_d0.9994487
X-RAY DIFFRACTIONf_dihedral_angle_d16.5031202
X-RAY DIFFRACTIONf_chiral_restr0.064524
X-RAY DIFFRACTIONf_plane_restr0.008596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7154-1.75830.2638830.28231678X-RAY DIFFRACTION54
1.7583-1.80590.29581430.24562816X-RAY DIFFRACTION91
1.8059-1.8590.251400.22082986X-RAY DIFFRACTION97
1.859-1.9190.26761560.22213017X-RAY DIFFRACTION97
1.919-1.98760.22441410.20873039X-RAY DIFFRACTION97
1.9876-2.06720.25131440.20522913X-RAY DIFFRACTION95
2.0672-2.16120.21771510.18723041X-RAY DIFFRACTION98
2.1612-2.27520.23041490.19443055X-RAY DIFFRACTION98
2.2752-2.41770.24051450.18833029X-RAY DIFFRACTION98
2.4177-2.60430.21221440.18242992X-RAY DIFFRACTION96
2.6043-2.86640.20381470.17933066X-RAY DIFFRACTION98
2.8664-3.28090.20871420.17063021X-RAY DIFFRACTION97
3.2809-4.13290.18221550.14443108X-RAY DIFFRACTION99
4.1329-38.72790.17181510.16273134X-RAY DIFFRACTION98

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