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Yorodumi- PDB-1l7m: HIGH RESOLUTION LIGANDED STRUCTURE OF PHOSPHOSERINE PHOSPHATASE (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l7m | ||||||
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Title | HIGH RESOLUTION LIGANDED STRUCTURE OF PHOSPHOSERINE PHOSPHATASE (PI COMPLEX) | ||||||
Components | Phosphoserine Phosphatase | ||||||
Keywords | HYDROLASE / Rossmann Fold / four-Helix bundle / b-hairpin / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center | ||||||
Function / homology | Function and homology information phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Wang, W. / Cho, H.S. / Kim, R. / Jancarik, J. / Yokota, H. / Nguyen, H.H. / Grigoriev, I.V. / Wemmer, D.E. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Structural characterization of the reaction pathway in phosphoserine phosphatase: crystallographic "snapshots" of intermediate states. Authors: Wang, W. / Cho, H.S. / Kim, R. / Jancarik, J. / Yokota, H. / Nguyen, H.H. / Grigoriev, I.V. / Wemmer, D.E. / Kim, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l7m.cif.gz | 105.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l7m.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 1l7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l7m_validation.pdf.gz | 433.5 KB | Display | wwPDB validaton report |
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Full document | 1l7m_full_validation.pdf.gz | 438.6 KB | Display | |
Data in XML | 1l7m_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 1l7m_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/1l7m ftp://data.pdbj.org/pub/pdb/validation_reports/l7/1l7m | HTTPS FTP |
-Related structure data
Related structure data | 1l7nC 1l7oC 1l7pC 1f5sS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23775.346 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: MJ1594 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B384(DE3)/pSJS1244 / References: UniProt: Q58989, phosphoserine phosphatase #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: 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: 2.68 Å3/Da / Density % sol: 53.74 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 22% PEG 200 MME, 0.2M SODIUM PHOSPHATE, 0.1M ACETATE BUFFER, 5mM MgCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 25K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Details: Wang, W., (2001) Struct. Fold. Des., 9, 65. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 3, 2000 |
Radiation | Monochromator: ALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→30 Å / Num. all: 70604 / Num. obs: 70604 / % possible obs: 0.989 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.9 Å2 / Rsym value: 0.035 / Net I/σ(I): 36 |
Reflection shell | Resolution: 1.48→1.5 Å / Mean I/σ(I) obs: 3.4 / Num. unique all: 3547 / Rsym value: 0.335 / % possible all: 0.974 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 72554 / % possible obs: 98.9 % / Rmerge(I) obs: 0.035 |
Reflection shell | *PLUS % possible obs: 97.4 % / Num. unique obs: 3547 / Rmerge(I) obs: 0.335 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F5S Resolution: 1.48→15 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: CNS
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Displacement parameters | Biso mean: 13.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.48→15 Å
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Refinement | *PLUS Lowest resolution: 15 Å / % reflection Rfree: 10 % / Rfactor obs: 0.202 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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