+Open data
-Basic information
Entry | Database: PDB / ID: 8s5r | |||||||||
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Title | Structure of the Chlamydia pneumoniae effector SemD | |||||||||
Components | Effector SemD | |||||||||
Keywords | ENDOCYTOSIS / effector effector protein | |||||||||
Function / homology | Uncharacterized protein Function and homology information | |||||||||
Biological species | Chlamydia (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Kocher, F. / Applegate, V. / Reiners, J. / Port, A. / Spona, D. / Haensch, S. / Smits, S.H. / Hegemann, J. / Moelleken, K. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: To Be Published Title: Structure of the Chlamydia pneumoniae effector SemD Authors: Kocher, F. / Applegate, V. / Reiners, J. / Port, A. / Spona, D. / Haensch, S. / Smits, S.H. / Hegemann, J. / Moelleken, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8s5r.cif.gz | 130.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8s5r.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 8s5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8s5r_validation.pdf.gz | 448.2 KB | Display | wwPDB validaton report |
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Full document | 8s5r_full_validation.pdf.gz | 454.2 KB | Display | |
Data in XML | 8s5r_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 8s5r_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/8s5r ftp://data.pdbj.org/pub/pdb/validation_reports/s5/8s5r | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (0.551977439338, 0.826944613355, 0.107161153899), (0.823340270627, -0.560843187638, 0.0869811338344), (0.132029183232, 0.0402184699273, -0.990429588336)Vector: -28. ...NCS oper: (Code: given Matrix: (0.551977439338, 0.826944613355, 0.107161153899), Vector: |
-Components
#1: Protein | Mass: 34331.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia (bacteria) Gene: CP_0070, CPn_0677, BN1224_CV15_C_01450, BN1224_GiD_A_07040, BN1224_H12_EK_00710, BN1224_MUL2216_F_02260, BN1224_Panola_J_01100, BN1224_PB1_B_06920, BN1224_U1271_C_05340, BN1224_Wien2_G_03310, ...Gene: CP_0070, CPn_0677, BN1224_CV15_C_01450, BN1224_GiD_A_07040, BN1224_H12_EK_00710, BN1224_MUL2216_F_02260, BN1224_Panola_J_01100, BN1224_PB1_B_06920, BN1224_U1271_C_05340, BN1224_Wien2_G_03310, BN1224_YK41_BR_01220, CWL029c_D_02120 Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z7M7 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M Citric acid (pH 2.5), 20% (w/v) PEG 6000 (pH 4) |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.916771 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 5, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916771 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45.82 Å / Num. obs: 51456 / % possible obs: 97.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.34 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.61 |
Reflection shell | Resolution: 2.1→2.175 Å / Mean I/σ(I) obs: 2.56 / Num. unique obs: 2675 / CC1/2: 0.939 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.82 Å / SU ML: 0.2786 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.3166 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→45.82 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.26105376419 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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