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Yorodumi- PDB-1eyz: STRUCTURE OF ESCHERICHIA COLI PURT-ENCODED GLYCINAMIDE RIBONUCLEO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eyz | ||||||
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Title | STRUCTURE OF ESCHERICHIA COLI PURT-ENCODED GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE COMPLEXED WITH MG AND AMPPNP | ||||||
Components | PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE 2 | ||||||
Keywords | TRANSFERASE / Transformylase / purine biosynthesis / ATP-grasp | ||||||
Function / homology | Function and homology information phosphoribosylglycinamide formyltransferase 2 / phosphoribosylglycinamide formyltransferase 2 activity / acetate kinase activity / phosphoribosylglycinamide formyltransferase activity / 'de novo' IMP biosynthetic process / ligase activity / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.75 Å | ||||||
Authors | Thoden, J.B. / Firestine, S. / Nixon, A. / Benkovic, S.J. / Holden, H.M. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase. Authors: Thoden, J.B. / Firestine, S. / Nixon, A. / Benkovic, S.J. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eyz.cif.gz | 184.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eyz.ent.gz | 143 KB | Display | PDB format |
PDBx/mmJSON format | 1eyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/1eyz ftp://data.pdbj.org/pub/pdb/validation_reports/ey/1eyz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a homodimer consisting of chains A & B |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 42480.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET-22B / Production host: Escherichia coli (E. coli) References: UniProt: P33221, Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases |
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-Non-polymers , 6 types, 857 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | #6: Chemical | ChemComp-MPO / | #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: 2.49 Å3/Da / Density % sol: 50.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: methylether PEG-5000, sodium chloride, magnesium chloride, 5'-adenylylimidodiphosphate, 3-(N-morpholino)propanesulfonic acid, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 25, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. all: 83396 / Num. obs: 83396 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.75→1.83 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.269 / Num. unique all: 9709 / % possible all: 90.8 |
Reflection | *PLUS Num. obs: 83063 |
Reflection shell | *PLUS % possible obs: 90.8 % / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Resolution: 1.75→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.75→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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