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Yorodumi- PDB-1j8d: Structure Of the metal-free form of the deoxy-D-mannose-octuloson... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j8d | ||||||
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Title | Structure Of the metal-free form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679) | ||||||
Components | deoxy-D-mannose-octulosonate 8-phosphate phosphatase | ||||||
Keywords | HYDROLASE / HI1679 / structural genomics / KDO 8-P phosphatase / Structure 2 Function Project / S2F | ||||||
Function / homology | Function and homology information 3-deoxy-manno-octulosonate-8-phosphatase / 3-deoxy-manno-octulosonate-8-phosphatase activity / lipopolysaccharide biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Haemophilus influenzae Rd (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Lim, K. / Herzberg, O. / Structure 2 Function Project (S2F) | ||||||
Citation | Journal: Proteins / Year: 2002 Title: From structure to function: YrbI from Haemophilus influenzae (HI1679) is a phosphatase. Authors: Parsons, J.F. / Lim, K. / Tempczyk, A. / Krajewski, W. / Eisenstein, E. / Herzberg, O. | ||||||
History |
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Remark 400 | COMPOUND THE FUNCTION OF THE PROTEIN WAS ASSIGNED INDEPENDENTLY BY THE WOODARD GROUP: ESCHERICHIA ...COMPOUND THE FUNCTION OF THE PROTEIN WAS ASSIGNED INDEPENDENTLY BY THE WOODARD GROUP: ESCHERICHIA COLI YRBI IS 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE, WU J, WOODARD RW; J BIOL CHEM. 2003 278:18117-2. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j8d.cif.gz | 143.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j8d.ent.gz | 123 KB | Display | PDB format |
PDBx/mmJSON format | 1j8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j8d_validation.pdf.gz | 473.2 KB | Display | wwPDB validaton report |
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Full document | 1j8d_full_validation.pdf.gz | 496.9 KB | Display | |
Data in XML | 1j8d_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 1j8d_validation.cif.gz | 45 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/1j8d ftp://data.pdbj.org/pub/pdb/validation_reports/j8/1j8d | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19783.549 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae Rd (bacteria) / Species: Haemophilus influenzae / Strain: KW20 / Gene: HI1679 / Plasmid: pDEST14-HI1679 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: P45314, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases #2: Chemical | ChemComp-GOL / | #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 Å3/Da / Density % sol: 38.38 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: protein (10 mg/ml) in 10mM NaHepes, pH 7.5, 1mM EDTA, 1mM DTT; crystallization in 22% polyethylene glycol 4000, 0.1 M Tris-HCl, 0.2 M Lithium sulfate. Glycerol added as cryoprotectant., pH 8. ...Details: protein (10 mg/ml) in 10mM NaHepes, pH 7.5, 1mM EDTA, 1mM DTT; crystallization in 22% polyethylene glycol 4000, 0.1 M Tris-HCl, 0.2 M Lithium sulfate. Glycerol added as cryoprotectant., pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 36 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X12C / Wavelength: 0.9790, 0.9787, 0.9500 | ||||||||||||
Detector | Type: BRANDEIS / Detector: CCD / Date: Aug 20, 2000 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→50 Å / Num. all: 28788 / Num. obs: 28788 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10 | ||||||||||||
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.171 / Num. unique all: 3494 / % possible all: 95.9 | ||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 158161 | ||||||||||||
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / % possible obs: 95.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 34 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å /
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5.9 % / Rfactor obs: 0.176 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.6 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.3 Å / Rfactor Rfree: 0.302 / Rfactor Rwork: 0.198 |