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- PDB-2yn3: Structural insight into the giant calcium-binding adhesin SiiE: i... -

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Basic information

Entry
Database: PDB / ID: 2yn3
TitleStructural insight into the giant calcium-binding adhesin SiiE: implications for the adhesion of Salmonella enterica to polarized epithelial cells
ComponentsPUTATIVE INNER MEMBRANE PROTEIN
KeywordsMEMBRANE PROTEIN / BIG-DOMAINS ADHESIN
Function / homology
Function and homology information


homophilic cell adhesion via plasma membrane adhesion molecules / calcium ion binding / membrane
Similarity search - Function
N-terminal domain of TfIIb - #90 / Bacterial Ig-like domain / Bacterial Ig-like domain 13 / Bacterial Ig-like domain / Ig-like domain, bacterial type / N-terminal domain of TfIIb / Cadherin-like / Cadherins domain profile. / Other non-globular / Special ...N-terminal domain of TfIIb - #90 / Bacterial Ig-like domain / Bacterial Ig-like domain 13 / Bacterial Ig-like domain / Ig-like domain, bacterial type / N-terminal domain of TfIIb / Cadherin-like / Cadherins domain profile. / Other non-globular / Special / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / PHOSPHATE ION / Inner membrane protein
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.12 Å
AuthorsGriessl, M.H. / Schmid, B. / Kassler, K. / Braunsmann, C. / Ritter, R. / Barlag, B. / Sturm, K.U. / Danzer, C. / Wagner, C. / Schaeffer, T.E. ...Griessl, M.H. / Schmid, B. / Kassler, K. / Braunsmann, C. / Ritter, R. / Barlag, B. / Sturm, K.U. / Danzer, C. / Wagner, C. / Schaeffer, T.E. / Sticht, H. / Hensel, M. / Muller, Y.A.
Citation
Journal: Structure / Year: 2013
Title: Structural Insight Into the Giant Ca(2+)-Binding Adhesin Siie: Implications for the Adhesion of Salmonella Enterica to Polarized Epithelial Cells.
Authors: Griessl, M.H. / Schmid, B. / Kassler, K. / Braunsmann, C. / Ritter, R. / Barlag, B. / Stierhof, Y. / Sturm, K.U. / Danzer, C. / Wagner, C. / Schaffer, T.E. / Sticht, H. / Hensel, M. / Muller, Y.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization and Preliminary Crystallographic Analysis of an Ig-Domain-Encompassing Fragment of the Giant Adhesion Protein Siie from Salmonella Enterica.
Authors: Sturm, K.U. / Griessl, M.H. / Wagner, C. / Deiwick, J. / Hensel, M. / Muller, Y.A.
History
DepositionOct 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _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
A: PUTATIVE INNER MEMBRANE PROTEIN
B: PUTATIVE INNER MEMBRANE PROTEIN
C: PUTATIVE INNER MEMBRANE PROTEIN
D: PUTATIVE INNER MEMBRANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,55720
Polymers121,6874
Non-polymers87016
Water8,323462
1
A: PUTATIVE INNER MEMBRANE PROTEIN
C: PUTATIVE INNER MEMBRANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,47312
Polymers60,8432
Non-polymers62910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-107.9 kcal/mol
Surface area26180 Å2
MethodPISA
2
B: PUTATIVE INNER MEMBRANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5424
Polymers30,4221
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: PUTATIVE INNER MEMBRANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5424
Polymers30,4221
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.480, 153.309, 96.300
Angle α, β, γ (deg.)90.00, 103.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
PUTATIVE INNER MEMBRANE PROTEIN / SIIE


Mass: 30421.697 Da / Num. of mol.: 4 / Fragment: BIG DOMAINS 50 TO 52, RESIDUES 5078-5365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
Strain: LT2 / Plasmid: P3355-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZKG6
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growDetails: 0.2 M AMMONIUM IODIDE, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9797
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 8, 2010 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.12→35 Å / Num. obs: 72931 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 10.7
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.9 / % possible all: 85.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.12→34.32 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.757 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25971 3648 5 %RANDOM
Rwork0.21024 ---
obs0.21271 69306 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.779 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å21.31 Å2
2---1.08 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.12→34.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7506 0 20 462 7988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.027640
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.95310499
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4925999
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32527.083312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.877151103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8021512
X-RAY DIFFRACTIONr_chiral_restr0.1020.21305
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215750
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 233 -
Rwork0.241 4435 -
obs--85.7 %

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