+Open data
-Basic information
Entry | Database: PDB / ID: 1l7o | ||||||
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Title | CRYSTAL STRUCTURE OF PHOSPHOSERINE PHOSPHATASE IN APO FORM | ||||||
Components | PHOSPHOSERINE PHOSPHATASE | ||||||
Keywords | HYDROLASE / Rossmann fold / beta-hairpin / four-helix bundle / 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: 2.2 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 | 1l7o.cif.gz | 96 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l7o.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 1l7o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l7o_validation.pdf.gz | 442.2 KB | Display | wwPDB validaton report |
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Full document | 1l7o_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 1l7o_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 1l7o_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/1l7o ftp://data.pdbj.org/pub/pdb/validation_reports/l7/1l7o | HTTPS FTP |
-Related structure data
Related structure data | 1l7mC 1l7nC 1l7pC 1f5sS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 23774.361 Da / Num. of mol.: 2 / Mutation: D11N 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): B834(DE3)/pSJS1244 / References: UniProt: Q58989, phosphoserine phosphatase #2: Chemical | #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: 54.16 % / Description: 0.2 degree oscillation angle |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 20mM Zinc acetate, 10% PEG 3350, 0.1M cacodylate buffer, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: Dec 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 26473 / Num. obs: 25996 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.32 Å2 / Rsym value: 0.077 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.2→2.38 Å / Mean I/σ(I) obs: 5.5 / Num. unique all: 1291 / Rsym value: 0.158 / % possible all: 85.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F5S Resolution: 2.2→15 Å / σ(F): 0 / Stereochemistry target values: CNS
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Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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