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Yorodumi- PDB-1qd1: THE CRYSTAL STRUCTURE OF THE FORMIMINOTRANSFERASE DOMAIN OF FORMI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qd1 | ||||||
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Title | THE CRYSTAL STRUCTURE OF THE FORMIMINOTRANSFERASE DOMAIN OF FORMIMINOTRANSFERASE-CYCLODEAMINASE. | ||||||
Components | FORMIMINOTRANSFERASE-CYCLODEAMINASE | ||||||
Keywords | TRANSFERASE / FUNCTIONAL DIMER / ALPHA-BETA-BETA-ALPHA SANDWICH / ELECTROSTATICALLY CHARGED SUBSTRATE TUNNEL | ||||||
Function / homology | Function and homology information glutamate formimidoyltransferase / formimidoyltetrahydrofolate cyclodeaminase / glutamate formimidoyltransferase activity / formimidoyltetrahydrofolate cyclodeaminase activity / L-histidine catabolic process / L-histidine catabolic process to glutamate and formamide / L-histidine catabolic process to glutamate and formate / tetrahydrofolate interconversion / folic acid binding / centriole / Golgi apparatus Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Kohls, D. / Sulea, T. / Purisima, E. / MacKenzie, R.E. / Vrielink, A. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: The crystal structure of the formiminotransferase domain of formiminotransferase-cyclodeaminase: implications for substrate channeling in a bifunctional enzyme. Authors: Kohls, D. / Sulea, T. / Purisima, E.O. / MacKenzie, R.E. / Vrielink, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qd1.cif.gz | 158.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qd1.ent.gz | 122.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/1qd1 ftp://data.pdbj.org/pub/pdb/validation_reports/qd/1qd1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35878.910 Da / Num. of mol.: 2 / Fragment: FORMIMINOTRANSFERASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Organ: liver / Plasmid: pBke-Cm1 / Production host: Escherichia coli (E. coli) References: UniProt: P53603, glutamate formimidoyltransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.92 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: sodium citrate, glycerol, tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.7→50 Å / Num. all: 89972 / Num. obs: 436554 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.85 % / Biso Wilson estimate: 20.92 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 20.5 | ||||||||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.186 / Num. unique all: 8547 / % possible all: 95.1 | ||||||||||||||||||
Reflection | *PLUS Num. obs: 89972 / Num. measured all: 436554 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 95.1 % |
-Processing
Software |
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Refinement | Resolution: 1.7→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: no NCS restraints imposed Parameter and topology files for the ligands, folinic acid and glycerol were obtained from the Heteroatom compound database (Upsala, Sweden). The stereochemistry ...Details: no NCS restraints imposed Parameter and topology files for the ligands, folinic acid and glycerol were obtained from the Heteroatom compound database (Upsala, Sweden). The stereochemistry for folinic acid was manually altered from 6S to 6R.
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.21 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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