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Yorodumi- PDB-1phq: Crystal structure of KDO8P synthase in its binary complex with su... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1phq | ||||||
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Title | Crystal structure of KDO8P synthase in its binary complex with substrate analog E-FPEP | ||||||
Components | 2-dehydro-3-deoxyphosphooctonate aldolase | ||||||
Keywords | TRANSFERASE / BETA-ALPHA-BARRELS / LYASE / LIPOPOLYSACCHARIDE / FLUORINATED ANALOG | ||||||
Function / homology | Function and homology information 3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / protein-containing complex / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Vainer, R. / Adir, N. / Baasov, T. / Belakhov, V. / Rabkin, E. | ||||||
Citation | Journal: To be Published Title: Crystallographic Analysis of the Phosphoenol Pyruvate Binding Site in E. Coli KDO8P Synthase Authors: Vainer, R. / Adir, N. / Baasov, T. / Belakhov, V. / Rabkin, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1phq.cif.gz | 66.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1phq.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 1phq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/1phq ftp://data.pdbj.org/pub/pdb/validation_reports/ph/1phq | HTTPS FTP |
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-Related structure data
Related structure data | 1d9eS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. The biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: x,y,z; -x,-y,z; -x,y,-z; x,y,-z; |
-Components
#1: Protein | Mass: 30870.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: KDSA / Production host: Escherichia coli (E. coli) References: UniProt: P0A715, 3-deoxy-8-phosphooctulonate synthase |
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#2: Chemical | ChemComp-FPE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG 4000, Glycrol, Tris-HCl , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 18, 2002 / Details: Bent mirror |
Radiation | Monochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. all: 7610 / Num. obs: 6714 / % possible obs: 88.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 91 / Num. unique all: 679 / Rsym value: 0.206 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1D9E (a) Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.82 Å
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