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Yorodumi- PDB-1rzm: Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rzm | ||||||
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Title | Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) from Thermotoga maritima complexed with Cd2+, PEP and E4P | ||||||
Components | Phospho-2-dehydro-3-deoxyheptonate aldolase | ||||||
Keywords | TRANSFERASE / (BETA/ALPHA) BARREL / TIM BARREL | ||||||
Function / homology | Function and homology information 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aldehyde-lyase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Shumilin, I.A. / Bauerle, R. / Wu, J. / Woodard, R.W. / Kretsinger, R.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystal Structure of the Reaction Complex of 3-Deoxy-d-arabino-heptulosonate-7-phosphate Synthase from Thermotoga maritima Refines the Catalytic Mechanism and Indicates a New Mechanism of Allosteric Regulation. Authors: Shumilin, I.A. / Bauerle, R. / Wu, J. / Woodard, R.W. / Kretsinger, R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rzm.cif.gz | 144.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rzm.ent.gz | 113.6 KB | Display | PDB format |
PDBx/mmJSON format | 1rzm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rzm_validation.pdf.gz | 468.8 KB | Display | wwPDB validaton report |
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Full document | 1rzm_full_validation.pdf.gz | 485.1 KB | Display | |
Data in XML | 1rzm_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 1rzm_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/1rzm ftp://data.pdbj.org/pub/pdb/validation_reports/rz/1rzm | HTTPS FTP |
-Related structure data
Related structure data | 1fwwS 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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Components on special symmetry positions |
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Details | The biological assembly is a tetramer |
-Components
#1: Protein | Mass: 37430.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: AROF, TM0343 / Plasmid: pT7-aroG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9WYH8, 3-deoxy-7-phosphoheptulonate synthase #2: Chemical | #3: Chemical | #4: Sugar | #5: 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: 2.43 Å3/Da / Density % sol: 49.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, LiCl, bis-tris propane, CdCl2, PEP, E4P, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.2831 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2002 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2831 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 37384 / Num. obs: 37384 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3708 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FWW Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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