[English] 日本語
Yorodumi- PDB-1kj9: Crystal structure of purt-encoded glycinamide ribonucleotide tran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kj9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of purt-encoded glycinamide ribonucleotide transformylase complexed with Mg-ATP | ||||||
Components | phosphoribosylglycinamide formyltransferase 2 | ||||||
Keywords | TRANSFERASE / ATP-grasp / purine biosynthesis / nucleotide | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Thoden, J.B. / Firestine, S.M. / Benkovic, S.J. / Holden, H.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site. Authors: Thoden, J.B. / Firestine, S.M. / Benkovic, S.J. / Holden, H.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kj9.cif.gz | 189.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kj9.ent.gz | 145.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/1kj9 ftp://data.pdbj.org/pub/pdb/validation_reports/kj/1kj9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1kj8C 1kjiC 1kjjC 1kjqC 1eyzS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 42349.340 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURT / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P33221, Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases |
---|
-Non-polymers , 7 types, 1011 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MPO / | #7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.75 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: batch / pH: 6.7 Details: PEG 5000, NaCl, MgCl2, MOPS, ATP, pH 6.7, batch at 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: batch method / Details: used macroseeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Apr 27, 2000 / Details: goebel optics |
Radiation | Monochromator: goebel optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. all: 106671 / Num. obs: 106671 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.6→1.67 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 3.6 / Num. unique all: 11879 / % possible all: 79 |
Reflection | *PLUS Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 79 % / Num. unique obs: 11879 / Rmerge(I) obs: 0.203 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1EYZ Resolution: 1.6→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.18 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.182 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|