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Yorodumi- PDB-1u5h: Structure of Citrate Lyase beta subunit from Mycobacterium tuberc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u5h | ||||||
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Title | Structure of Citrate Lyase beta subunit from Mycobacterium tuberculosis | ||||||
Components | citECitation | ||||||
Keywords | LYASE / TIM barrel / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information Lyases; Carbon-carbon lyases / oxaloacetate metabolic process / lyase activity / magnesium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | Goulding, C.W. / Lekin, T. / Kim, C.Y. / Segelke, B. / Terwilliger, T.C. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: The structure and computational analysis of Mycobacterium tuberculosis protein CitE suggest a novel enzymatic function. Authors: Goulding, C.W. / Bowers, P.M. / Segelke, B. / Lekin, T. / Kim, C.Y. / Terwilliger, T.C. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u5h.cif.gz | 56.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u5h.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 1u5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/1u5h ftp://data.pdbj.org/pub/pdb/validation_reports/u5/1u5h | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28578.303 Da / Num. of mol.: 1 / Mutation: R20A, K23A, R222A, R223A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv2498c / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 References: UniProt: O06162, UniProt: P9WPE1*PLUS, citrate (pro-3S)-lyase |
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#2: Chemical | ChemComp-FMT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.6 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: sodium Formate, DMSO, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2002 |
Radiation | Monochromator: Si(220) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→100 Å / Num. obs: 5589 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.9 Å2 |
Reflection shell | Resolution: 1.65→1.75 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.65→19.67 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2122760.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.3651 Å2 / ksol: 0.440754 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→19.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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