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Yorodumi- PDB-1u5v: Structure of CitE complexed with triphosphate group of ATP form M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u5v | ||||||
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Title | Structure of CitE complexed with triphosphate group of ATP form 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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Goulding, C.W. / Lerkin, T. / Kim, C.Y. / Segelke, B. / Terwilliger, T. / Eisenberg, E. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Mycobacterium tuberculosis citrate lyase beta subunit and its unusual triphosphate binding site Authors: Goulding, C.W. / Lerkin, T. / Kim, C.Y. / Segelke, B. / Terwilliger, T. / Eisenberg, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u5v.cif.gz | 59.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u5v.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 1u5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/1u5v ftp://data.pdbj.org/pub/pdb/validation_reports/u5/1u5v | HTTPS FTP |
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-Related structure data
Related structure data | 1u5hS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28520.268 Da / Num. of mol.: 1 / Mutation: R20A, K23A, R222A, P223A 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-ATP / |
#3: Chemical | ChemComp-FMT / |
#4: 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: 3.09 Å3/Da / Density % sol: 60.21 % |
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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 source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.04 Å |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 2003 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→100 Å / Num. all: 30274 / Num. obs: 30000 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 25.1 Å2 |
Reflection shell | Resolution: 1.85→1.95 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1U5H Resolution: 1.85→45.61 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 320557.21 / 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: 49.5023 Å2 / ksol: 0.357998 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→45.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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