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- PDB-1kjj: Crystal structure of glycniamide ribonucleotide transformylase in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kjj | ||||||
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Title | Crystal structure of glycniamide ribonucleotide transformylase in complex with Mg-ATP-gamma-S | ||||||
![]() | phosphoribosylglycinamide formyltransferase 2 | ||||||
![]() | TRANSFERASE / ATP-grasp / purine biosynthesis / nucleotide | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thoden, J.B. / Firestine, S.M. / Benkovic, S.J. / Holden, H.M. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.4 KB | Display | ![]() |
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PDB format | ![]() | 138.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 40.3 KB | Display | |
Data in CIF | ![]() | 59.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kj8C ![]() 1kj9C ![]() 1kjiC ![]() 1kjqC ![]() 1eyzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() ![]() References: UniProt: P33221, Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases |
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-Non-polymers , 6 types, 683 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/AGS.gif)
![](data/chem/img/MPO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/AGS.gif)
![](data/chem/img/MPO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / | #5: Chemical | #6: Chemical | ChemComp-MPO / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.64 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: batch / pH: 6.7 Details: PEG 5000, NaCl, MgCl2, MOPS, ATP-gamma-S, pH 6.7, batch at 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: batch method / Details: used macroseeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Nov 6, 2000 / Details: goebel optics |
Radiation | Monochromator: goebel optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. all: 82695 / Num. obs: 82695 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.75→1.87 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 4.4 / Num. unique all: 9407 / % possible all: 88 |
Reflection | *PLUS Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 88 % / Num. unique obs: 9407 / Rmerge(I) obs: 0.215 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EYZ Resolution: 1.75→30 Å / Cross valid method: THROUGHOUT / σ(F): 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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Refinement | *PLUS Rfactor all: 0.187 / Rfactor Rfree: 0.233 / Rfactor Rwork: 0.184 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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