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Yorodumi- PDB-1grc: CRYSTAL STRUCTURE OF GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE FR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1grc | ||||||
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Title | CRYSTAL STRUCTURE OF GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE FROM ESCHERICHIA COLI AT 3.0 ANGSTROMS RESOLUTION: A TARGET ENZYME FOR CHEMOTHERAPY | ||||||
Components | GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE | ||||||
Keywords | TRANSFERASE(FORMYL) | ||||||
Function / homology | Function and homology information phosphoribosylglycinamide formyltransferase 1 / phosphoribosylglycinamide formyltransferase activity / 'de novo' IMP biosynthetic process / DNA damage response / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | ||||||
Authors | Chen, P. / Wilson, I.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1992 Title: Crystal structure of glycinamide ribonucleotide transformylase from Escherichia coli at 3.0 A resolution. A target enzyme for chemotherapy. Authors: Chen, P. / Schulze-Gahmen, U. / Stura, E.A. / Inglese, J. / Johnson, D.L. / Marolewski, A. / Benkovic, S.J. / Wilson, I.A. #1: Journal: J.Biol.Chem. / Year: 1989 Title: Preliminary Crystallographic Investigations of Glycinamide Ribonucleotide Transformylase in Escherichia Coli K12 Authors: Stura, E.A. / Johnson, D.L. / Inglese, J. / Smith, J.M. / Benkovic, S.J. / Wilson, I.A. #2: Journal: J.Biol.Chem. / Year: 1987 Title: Identification and Nucleotide Sequence of a Gene Encoding 5'-Phosphoribosyl-Glycinamide Transformylase in Escherichia Coli K12 Authors: Smith, J.M. / Daum III, H.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1grc.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1grc.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 1grc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/1grc ftp://data.pdbj.org/pub/pdb/validation_reports/gr/1grc | 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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Atom site foot note | 1: RESIDUE 113 OF CHAIN B IS A CIS PROLINE. | ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. (KABSCH ROTATION MATRIX) THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. (KABSCH ROTATION MATRIX) |
-Components
#1: Protein | Mass: 23266.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain (production host): K12 References: UniProt: P08179, phosphoribosylglycinamide formyltransferase 1 #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 67.86 % | |||||||||||||||
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Crystal grow | *PLUS pH: 6.75 / Method: vapor diffusion | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 3 Å / Num. obs: 13910 / % possible obs: 94.7 % / Num. measured all: 75626 / Rmerge(I) obs: 0.103 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.19 / Rfactor obs: 0.19 / Highest resolution: 3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.55 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.1 Å / Rfactor obs: 0.27 |