+Open data
-Basic information
Entry | Database: PDB / ID: 1p9o | ||||||
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Title | Crystal Structure of Phosphopantothenoylcysteine Synthetase | ||||||
Components | Phosphopantothenoylcysteine synthetasePhosphopantothenate—cysteine ligase | ||||||
Keywords | LIGASE / synthetase | ||||||
Function / homology | Function and homology information phosphopantothenate-cysteine ligase (ATP) / phosphopantothenate--cysteine ligase activity / Coenzyme A biosynthesis / acetyl-CoA biosynthetic process / heart process / coenzyme A biosynthetic process / protein homodimerization activity / ATP binding / identical protein binding / nucleus ...phosphopantothenate-cysteine ligase (ATP) / phosphopantothenate--cysteine ligase activity / Coenzyme A biosynthesis / acetyl-CoA biosynthetic process / heart process / coenzyme A biosynthetic process / protein homodimerization activity / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Manoj, N. / Strauss, E. / Begley, T.P. / Ealick, S.E. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Structure of human phosphopantothenoylcysteine synthetase at 2.3 A resolution. Authors: Manoj, N. / Strauss, E. / Begley, T.P. / Ealick, S.E. | ||||||
History |
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Remark 999 | SEQUENCE an appropriate sequence database reference for the protein was not available at the time ...SEQUENCE an appropriate sequence database reference for the protein was not available at the time of processing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p9o.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p9o.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 1p9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/1p9o ftp://data.pdbj.org/pub/pdb/validation_reports/p9/1p9o | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The crystallographic asymmetric unit contains two chains forming a homodimer that represents the biological unit |
-Components
#1: Protein | Mass: 34164.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: coaB / Plasmid: pPROEX-Hta / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: Q9HAB8, phosphopantothenate-cysteine ligase (CTP) #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 | Density Matthews: 2.76 Å3/Da / Density % sol: 55.4 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG MME 2000, Ammonium Sulphate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2002 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 35261 / Num. obs: 34732 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 34 Å2 / Rsym value: 0.064 / Net I/σ(I): 31.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 6.3 / Num. unique all: 3418 / Rsym value: 0.313 / % possible all: 99.7 |
Reflection | *PLUS Num. measured all: 199382 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.313 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SAD phased structure of phosphopantothenoylcysteine synthetase Resolution: 2.3→45.32 Å / Rfactor Rfree error: 0.005 / 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: 60.9858 Å2 / ksol: 0.35878 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→45.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 50 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.271 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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