+Open data
-Basic information
Entry | Database: PDB / ID: 1xho | ||||||
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Title | Chorismate mutase from Clostridium thermocellum Cth-682 | ||||||
Components | Chorismate mutase | ||||||
Keywords | structural genomics / unknown function / Chorismate mutase / Clostridium thermocellum / Southeast Collaboratory for Structural Genomics / SECSG / protein structure initiative / PSI | ||||||
Function / homology | Function and homology information chorismate metabolic process / chorismate mutase / chorismate mutase activity / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Clostridium thermocellum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / sad / Resolution: 2.2 Å | ||||||
Authors | Xu, H. / Chen, L. / Lee, D. / Habel, J.E. / Nguyen, J. / Chang, S.-H. / Kataeva, I. / Chang, J. / Zhao, M. / Yang, H. ...Xu, H. / Chen, L. / Lee, D. / Habel, J.E. / Nguyen, J. / Chang, S.-H. / Kataeva, I. / Chang, J. / Zhao, M. / Yang, H. / Horanyi, P. / Florence, Q. / Tempel, W. / Zhou, W. / Lin, D. / Zhang, H. / Praissman, J. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Ljungdahl, L. / Liu, Z.-J. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Away from the edge II: in-house Se-SAS phasing with chromium radiation. Authors: Xu, H. / Yang, C. / Chen, L. / Kataeva, I.A. / Tempel, W. / Lee, D. / Habel, J.E. / Nguyen, D. / Pflugrath, J.W. / Ferrara, J.D. / Arendall, W.B. / Richardson, J.S. / Richardson, D.C. / Liu, ...Authors: Xu, H. / Yang, C. / Chen, L. / Kataeva, I.A. / Tempel, W. / Lee, D. / Habel, J.E. / Nguyen, D. / Pflugrath, J.W. / Ferrara, J.D. / Arendall, W.B. / Richardson, J.S. / Richardson, D.C. / Liu, Z.J. / Newton, M.G. / Rose, J.P. / Wang, B.C. | ||||||
History |
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Remark 300 | BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xho.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xho.ent.gz | 61.4 KB | Display | PDB format |
PDBx/mmJSON format | 1xho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/1xho ftp://data.pdbj.org/pub/pdb/validation_reports/xh/1xho | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16699.916 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 48857462, UniProt: A3DDB7*PLUS #2: Chemical | #3: 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: 291 K / pH: 7.6 Details: 2.5M ammonium sulfate, 0.1M HEPES, pH 7.6, vapor diffusion, temperature 291K, pH 7.60 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 2.29 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.29 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→10 Å / Num. obs: 15073 / % possible obs: 93.3 % / Rmerge(I) obs: 0.057 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.167 / % possible all: 42.9 |
-Phasing
Phasing | Method: sad | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD | D res high: 2.4 Å / D res low: 20 Å / FOM : 0.39 / Reflection: 12228 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing MAD shell |
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Phasing dm | FOM : 0.54 / FOM acentric: 0.54 / FOM centric: 0 / Reflection: 14517 / Reflection acentric: 14517 / Reflection centric: 0 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→9.96 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: THROUGHOUT / ESU R Free: 0.246 / Stereochemistry target values: ENGH & HUBER / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.82 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→9.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.25 Å / Total num. of bins used: 20
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