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Yorodumi- PDB-1qzu: crystal structure of human phosphopantothenoylcysteine decarboxylase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qzu | ||||||
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Title | crystal structure of human phosphopantothenoylcysteine decarboxylase | ||||||
Components | hypothetical protein MDS018 | ||||||
Keywords | LYASE / alpha-beta sandwich | ||||||
Function / homology | Function and homology information phosphopantothenoylcysteine decarboxylase / phosphopantothenoylcysteine decarboxylase complex / phosphopantothenoylcysteine decarboxylase activity / Coenzyme A biosynthesis / coenzyme A biosynthetic process / FMN binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | ||||||
Authors | Manoj, N. / Ealick, S.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Unusual space-group pseudosymmetry in crystals of human phosphopantothenoylcysteine decarboxylase. Authors: Manoj, N. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qzu.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qzu.ent.gz | 93.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qzu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qzu_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1qzu_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1qzu_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 1qzu_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/1qzu ftp://data.pdbj.org/pub/pdb/validation_reports/qz/1qzu | HTTPS FTP |
-Related structure data
Related structure data | 1e20S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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Unit cell |
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Details | The biological assembly is a trimer generated from a monomer in the asymmetric unit by the operations: -X+Y+1,-X+1,Z and -Y+1,X-Y,Z |
-Components
#1: Protein | Mass: 22566.322 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: coac / Plasmid: PPROEX-HTA / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: Q96CD2, phosphopantothenoylcysteine decarboxylase #2: Chemical | ChemComp-FMN / |
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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: 2.55 Å3/Da / Density % sol: 51.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: ammonium sulphate, dioxane, 2-(N-Morpholino)ethane sulfonic acid, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9876 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9876 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. all: 18689 / Num. obs: 18689 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 107.5 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1886 / Rsym value: 0.034 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1E20 Resolution: 2.91→25.48 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The coordinates in this entry should be used with caution because of the larger coordinate error and a higher R-factor. These coordinates were used to report the facts presented in the primary citation.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 75.9587 Å2 / ksol: 0.256518 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.91→25.48 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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