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- PDB-6eff: NCTC10712 -

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Basic information

Entry
Database: PDB / ID: 6eff
TitleNCTC10712
ComponentsNCTC10712 Siglec
KeywordsSUGAR BINDING PROTEIN / lectin
Function / homologyUbiquitin-like (UB roll) - #890 / Ubiquitin-like (UB roll) / Roll / Alpha Beta / ACETATE ION
Function and homology information
Biological speciesStreptococcus mitis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 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: Advisory / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NCTC10712 Siglec
B: NCTC10712 Siglec
C: NCTC10712 Siglec
D: NCTC10712 Siglec
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,15131
Polymers92,1134
Non-polymers2,03727
Water17,799988
1
A: NCTC10712 Siglec
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4777
Polymers23,0281
Non-polymers4496
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NCTC10712 Siglec
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6289
Polymers23,0281
Non-polymers6008
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NCTC10712 Siglec
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2935
Polymers23,0281
Non-polymers2644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NCTC10712 Siglec
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,75310
Polymers23,0281
Non-polymers7259
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.786, 48.268, 99.823
Angle α, β, γ (deg.)101.84, 91.39, 89.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
NCTC10712 Siglec


Mass: 23028.367 Da / Num. of mol.: 4 / Fragment: residues 242-450
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mitis (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 988 / 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: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 7.5, 32% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 96441 / % possible obs: 92.4 % / Redundancy: 3.6 % / Net I/σ(I): 22.9
Reflection shellResolution: 1.6→1.64 Å

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Processing

SoftwareName: PHENIX / Version: (1.12_2829) / Classification: refinement
RefinementResolution: 1.6→47.241 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.66
RfactorNum. reflection% reflection
Rfree0.2078 4400 4.97 %
Rwork0.1803 --
obs0.1817 88590 92.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→47.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6309 0 120 988 7417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066653
X-RAY DIFFRACTIONf_angle_d0.9249115
X-RAY DIFFRACTIONf_dihedral_angle_d15.3582469
X-RAY DIFFRACTIONf_chiral_restr0.0571061
X-RAY DIFFRACTIONf_plane_restr0.0081214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.30121120.29392030X-RAY DIFFRACTION68
1.6182-1.63720.31081470.26762338X-RAY DIFFRACTION77
1.6372-1.65720.30561420.25042786X-RAY DIFFRACTION91
1.6572-1.67820.3281560.25322775X-RAY DIFFRACTION94
1.6782-1.70030.30371410.24452867X-RAY DIFFRACTION94
1.7003-1.72360.27471520.22852973X-RAY DIFFRACTION95
1.7236-1.74820.27121450.22172823X-RAY DIFFRACTION94
1.7482-1.77430.22631690.2132842X-RAY DIFFRACTION95
1.7743-1.8020.27641720.21252875X-RAY DIFFRACTION94
1.802-1.83150.23381500.19592837X-RAY DIFFRACTION94
1.8315-1.86310.2351520.19692879X-RAY DIFFRACTION94
1.8631-1.8970.20031450.18572905X-RAY DIFFRACTION93
1.897-1.93350.19611470.18272844X-RAY DIFFRACTION95
1.9335-1.9730.24291470.18272827X-RAY DIFFRACTION94
1.973-2.01590.20541550.17792839X-RAY DIFFRACTION93
2.0159-2.06280.18181470.17252832X-RAY DIFFRACTION94
2.0628-2.11430.18911290.172906X-RAY DIFFRACTION93
2.1143-2.17150.17491490.1672803X-RAY DIFFRACTION93
2.1715-2.23540.22611320.16522791X-RAY DIFFRACTION92
2.2354-2.30760.20081340.16692831X-RAY DIFFRACTION92
2.3076-2.390.17891600.17212767X-RAY DIFFRACTION92
2.39-2.48570.19941460.17362781X-RAY DIFFRACTION91
2.4857-2.59880.17131520.16762745X-RAY DIFFRACTION91
2.5988-2.73580.20391600.17082779X-RAY DIFFRACTION92
2.7358-2.90720.20441380.17752786X-RAY DIFFRACTION92
2.9072-3.13170.23131280.17412846X-RAY DIFFRACTION93
3.1317-3.44670.19251880.16292896X-RAY DIFFRACTION96
3.4467-3.94530.191240.15683005X-RAY DIFFRACTION98
3.9453-4.96970.16171550.15562954X-RAY DIFFRACTION97
4.9697-47.26170.22641260.21393028X-RAY DIFFRACTION99

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