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Yorodumi- PDB-1ecj: ESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ecj | ||||||
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Title | ESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMIDOTRANSFERASE COMPLEXED WITH 2 AMP PER TETRAMER | ||||||
Components | GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE | ||||||
Keywords | TRANSFERASE / GLUTAMINE AMIDOTRANSFERASE / PURINE BIOSYNTHESIS / GLYCOSYLTRANSFERASE / AMP / ADENINE 5'-MONOPHOSPHATE | ||||||
Function / homology | Function and homology information amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / guanosine tetraphosphate binding / glutamine metabolic process / glycosyltransferase activity / magnesium ion binding / identical protein binding ...amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / guanosine tetraphosphate binding / glutamine metabolic process / glycosyltransferase activity / magnesium ion binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Muchmore, C.R. / Krahn, J.M. / Smith, J.L. | ||||||
Citation | Journal: Protein Sci. / Year: 1998 Title: Crystal structure of glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli. Authors: Muchmore, C.R. / Krahn, J.M. / Kim, J.H. / Zalkin, H. / Smith, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ecj.cif.gz | 382.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ecj.ent.gz | 316 KB | Display | PDB format |
PDBx/mmJSON format | 1ecj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/1ecj ftp://data.pdbj.org/pub/pdb/validation_reports/ec/1ecj | HTTPS FTP |
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-Related structure data
Related structure data | 1ecfC 1gphS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 56422.684 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURF / Plasmid: PT7F1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P00496, UniProt: P0AG16*PLUS, amidophosphoribosyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 10 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 47.6 % Description: THE SYNCHROTRON DATA DESCRIBED BY THE PREVIOUS STATISTICS WAS SUPPLEMENTED WITH LOW RESOLUTION DATA COLLECTED WITH A RIGAKU ROTATING ANODE COPPER K(ALPHA) SOURCE AND A XUONG-HAMLIN ...Description: THE SYNCHROTRON DATA DESCRIBED BY THE PREVIOUS STATISTICS WAS SUPPLEMENTED WITH LOW RESOLUTION DATA COLLECTED WITH A RIGAKU ROTATING ANODE COPPER K(ALPHA) SOURCE AND A XUONG-HAMLIN MULTIWIRE AREA DETECTOR. THIS DATA WAS PROCESSED WITH XDS (KABSCH) ADAPTED FOR THE XUONG-HAMLIN DETECTOR (D. DIGGS, K. WATKINS). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.3 Details: 100MM MES, 50MM TRIS, 2MM AMP, 4MM EDTA, 15-18% PEG-3350, PH 6.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 27 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 279 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Feb 1, 1992 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 55291 / % possible obs: 77.8 % / Redundancy: 3.6 % / Rsym value: 0.065 / Net I/σ(I): 37 |
Reflection shell | Resolution: 2.5→2.61 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.215 / % possible all: 56.1 |
Reflection | *PLUS Num. measured all: 199847 / Rmerge(I) obs: 0.065 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GPH Resolution: 2.5→30 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: FREE R, THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS BETWEEN SUBUNIT FRAGMENTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 54315 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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