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Yorodumi- PDB-1k1e: Structure Of the cobalt-bound form of the deoxy-D-mannose-octulos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k1e | ||||||
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Title | Structure Of the cobalt-bound 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 / MOLECULAR REPLACEMENT / Resolution: 1.67 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 | 1k1e.cif.gz | 437.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k1e.ent.gz | 352.7 KB | Display | PDB format |
PDBx/mmJSON format | 1k1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/1k1e ftp://data.pdbj.org/pub/pdb/validation_reports/k1/1k1e | HTTPS FTP |
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-Related structure data
Related structure data | 1j8dSC 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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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 unit is a tetramer. The asymmetric unit contains three tetramers |
-Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 19455.283 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae Rd (bacteria) / Species: Haemophilus influenzae / Strain: KW20 / Gene: HI1679 / Plasmid: PDEST17-HI1679 / Production host: Escherichia coli (E. coli) / Strain (production host): B21(DE3) References: UniProt: P45314, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases |
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-Non-polymers , 6 types, 1465 molecules
#2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-HG / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: 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: 2.18 Å3/Da / Density % sol: 43.57 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.5 M ammonium sulfate, 0.1 M MES, 10 mM CoCl2. Crystal soaked with 1mM Hg acetate for 3 days. 10% glycerol added for flash-cooling, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95 Å |
Detector | Type: BRANDEIS / Detector: CCD / Date: Aug 20, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→50 Å / Num. all: 199616 / Num. obs: 199616 / % possible obs: 86.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.67→1.75 Å / Rmerge(I) obs: 0.213 / % possible all: 49.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HI1679 (PDB code 1j8d) Resolution: 1.67→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 21 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.75 Å / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.206 |