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Yorodumi- PDB-4mpo: 1.90 A resolution structure of CT771 from Chlamydia trachomatis B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mpo | ||||||
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Title | 1.90 A resolution structure of CT771 from Chlamydia trachomatis Bound to Hydrolyzed Ap4A Products | ||||||
Components | CT771 | ||||||
Keywords | HYDROLASE / hypothetical protein / Nudix / Ap4A / binary complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chlamydia trachomatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Barta, M.L. / Lovell, S. / Battaile, K.P. / Hefty, P.S. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Chlamydia trachomatis CT771 (nudH) Is an Asymmetric Ap4A Hydrolase. Authors: Barta, M.L. / Lovell, S. / Sinclair, A.N. / Battaile, K.P. / Hefty, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mpo.cif.gz | 260.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mpo.ent.gz | 205.6 KB | Display | PDB format |
PDBx/mmJSON format | 4mpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/4mpo ftp://data.pdbj.org/pub/pdb/validation_reports/mp/4mpo | HTTPS FTP |
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-Related structure data
Related structure data | 4ilqSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 17667.928 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: 434/Bu / Gene: CTL0140 / Plasmid: pTBSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: B0B8Z7, UniProt: A0A0H3MCJ9*PLUS, Hydrolases |
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-Non-polymers , 5 types, 375 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-AMP / #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-MG / #6: 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 | Density Matthews: 2.16 Å3/Da / Density % sol: 43.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, 25% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→91.038 Å / Num. all: 94728 / Num. obs: 93781 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ILQ Resolution: 1.9→39.627 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 1.33 / Phase error: 28.95 / Stereochemistry target values: ML
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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: 58.0155 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→39.627 Å
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Refine LS restraints |
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LS refinement shell |
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