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Basic information

Entry
Database: PDB / ID: 8ssk
TitleCitrobacter rodentium contact dependent growth inhibition (CDI) entry and toxin (CdiA-CT) domains
ComponentsFimbrial usher protein StbD
KeywordsTOXIN / Peptidase
Function / homology
Function and homology information


catalytic activity / toxin activity
Similarity search - Function
Toxin CdiA-like, Filamentous hemagglutinin motif repeats / VENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat / Pectin lyase fold / Pectin lyase fold/virulence factor / BRCT domain profile. / BRCT domain
Similarity search - Domain/homology
ACETATE ION / Fimbrial usher protein StbD
Similarity search - Component
Biological speciesCitrobacter rodentium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCuthbert, B.J. / Goulding, C.W. / Hayes, C.S. / Nhan, D.Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Citrobacter rodentium contact dependent growth inhibition (CDI) entry and toxin (CdiA-CT) domains
Authors: Cuthbert, B.J. / Goulding, C.W. / Hayes, C.S. / Nhan, D.Q.
History
DepositionMay 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.0Mar 5, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_modification_feature / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_modification_feature.auth_seq_id / _pdbx_modification_feature.modified_residue_auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Revision 3.0Apr 2, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / entity / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _cell.angle_beta / _cell.volume ..._cell.angle_beta / _cell.volume / _entity.pdbx_description / _pdbx_modification_feature.auth_seq_id / _pdbx_modification_feature.label_alt_id / _pdbx_modification_feature.modified_residue_auth_seq_id / _pdbx_modification_feature.modified_residue_label_alt_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.percent_reflns_obs / _software.version / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Description: Model orientation/position
Details: We wanted to simplify the modeling/occupancy of the disulfide bond between C70 and C77 for ease of discussion.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fimbrial usher protein StbD
B: Fimbrial usher protein StbD
C: Fimbrial usher protein StbD
D: Fimbrial usher protein StbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,69037
Polymers134,3064
Non-polymers2,38433
Water22,5191250
1
A: Fimbrial usher protein StbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1118
Polymers33,5761
Non-polymers5347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fimbrial usher protein StbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0117
Polymers33,5761
Non-polymers4346
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fimbrial usher protein StbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,40613
Polymers33,5761
Non-polymers83012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fimbrial usher protein StbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1629
Polymers33,5761
Non-polymers5868
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20290 Å2
ΔGint-237 kcal/mol
Surface area47180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.870, 113.982, 87.351
Angle α, β, γ (deg.)90.000, 92.388, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Fimbrial usher protein StbD / CdiA-PT/CT


Mass: 33576.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter rodentium (bacteria) / Gene: stbD, E2R62_11320 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A482PFX0

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Non-polymers , 5 types, 1283 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1250 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M sodium acetate, pH 4, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→39.26 Å / Num. obs: 101283 / % possible obs: 98.5 % / Redundancy: 7 % / Biso Wilson estimate: 22.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.074 / Rrim(I) all: 0.14 / Χ2: 0.98 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 7 % / Rmerge(I) obs: 1.187 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4996 / CC1/2: 0.746 / Rpim(I) all: 0.748 / Rrim(I) all: 1.409 / Χ2: 0.99 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→39.26 Å / SU ML: 0.1846 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.245
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1937 10055 9.94 %
Rwork0.166 91125 -
obs0.1688 101180 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8802 0 146 1250 10198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00469212
X-RAY DIFFRACTIONf_angle_d0.650812512
X-RAY DIFFRACTIONf_chiral_restr0.04241378
X-RAY DIFFRACTIONf_plane_restr0.00451640
X-RAY DIFFRACTIONf_dihedral_angle_d14.2333187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.31523320.27083007X-RAY DIFFRACTION98.09
1.92-1.940.29043270.24783028X-RAY DIFFRACTION98.59
1.94-1.970.26193460.23633073X-RAY DIFFRACTION98.84
1.97-1.990.25283310.22462992X-RAY DIFFRACTION98.43
1.99-2.020.2713380.22213018X-RAY DIFFRACTION98.24
2.02-2.050.26013230.21663035X-RAY DIFFRACTION98.3
2.05-2.080.24873270.21233009X-RAY DIFFRACTION96.75
2.08-2.110.24343340.20092890X-RAY DIFFRACTION94.99
2.11-2.140.21613360.1883058X-RAY DIFFRACTION99.09
2.14-2.170.21863390.18523075X-RAY DIFFRACTION99.56
2.17-2.210.21113250.17313064X-RAY DIFFRACTION99.47
2.21-2.250.20623320.17343068X-RAY DIFFRACTION99.24
2.25-2.30.19573560.1673030X-RAY DIFFRACTION98.92
2.3-2.340.19823260.16043046X-RAY DIFFRACTION98.71
2.34-2.390.21283310.16533072X-RAY DIFFRACTION98.52
2.39-2.450.2173320.16443007X-RAY DIFFRACTION98.18
2.45-2.510.21433330.17012971X-RAY DIFFRACTION97.18
2.51-2.580.22383300.17253010X-RAY DIFFRACTION96.45
2.58-2.650.20363420.16783056X-RAY DIFFRACTION99.3
2.65-2.740.19923380.16153040X-RAY DIFFRACTION99.29
2.74-2.840.17053360.15343066X-RAY DIFFRACTION99.21
2.84-2.950.1683310.15933074X-RAY DIFFRACTION99.27
2.95-3.090.21193450.16693055X-RAY DIFFRACTION98.89
3.09-3.250.19893390.16242995X-RAY DIFFRACTION97.69
3.25-3.450.16883330.15253011X-RAY DIFFRACTION96.96
3.45-3.720.16693400.14683102X-RAY DIFFRACTION99.65
3.72-4.090.14423360.12843058X-RAY DIFFRACTION99.04
4.09-4.680.13513400.12193074X-RAY DIFFRACTION98.53
4.68-5.90.18293390.15523047X-RAY DIFFRACTION97.95
5.9-39.260.19263380.1873094X-RAY DIFFRACTION97.53

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