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Yorodumi- PDB-1ecc: ESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ecc | ||||||
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Title | ESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMIDOTRANSFERASE COMPLEXED WITH MN-CPRPP AND 5-OXO-NORLEUCINE | ||||||
Components | GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE | ||||||
Keywords | TRANSFERASE / GLUTAMINE AMIDOTRANSFERASE / PURINE BIOSYNTHESIS / GLYCOSYLTRANSFERASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Krahn, J.M. / Smith, J.L. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Coupled formation of an amidotransferase interdomain ammonia channel and a phosphoribosyltransferase active site. Authors: Krahn, J.M. / Kim, J.H. / Burns, M.R. / Parry, R.J. / 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 | 1ecc.cif.gz | 206.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ecc.ent.gz | 168.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ecc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/1ecc ftp://data.pdbj.org/pub/pdb/validation_reports/ec/1ecc | HTTPS FTP |
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-Related structure data
Related structure data | 1ecbC 1ecfS 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.142832, 0.84025, 0.523047), Vector: |
-Components
#1: Protein | Mass: 56422.684 Da / Num. of mol.: 2 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 | ChemComp-MN / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | A WELL ORDERED MN++ EXISTS AT A LATTICE CONTACT. THIS METAL IS LIGATED TO GLU B 449, ASP B 471, AND ...A WELL ORDERED MN++ EXISTS AT A LATTICE CONTACT. THIS METAL IS LIGATED TO GLU B 449, ASP B 471, AND WATERS HOH A 507, HOH A 508, HOH B 507, AND HOH B 508. LIGATION TO ASP B 471 IS TO A SYMMETRY-EQUIVALENT | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46 % Description: A SINGLE GAT DOMAIN (249 RESIDUES) WAS USED AS THE PROBE MODEL DUE TO ALLOSTERIC DIFFERENCES BETWEEN THIS STRUCTURE AND THAT OF 1ECF. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.8 Details: 0.42MM CPRPP, 25MM MNCL2, 40MM BIS-TRIS PH 5.8, 3.2% 2-PROPANOL, 7.5% PEG-3350 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 15, 1996 |
Radiation | Monochromator: MSC DOUBLE MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→25 Å / Num. obs: 27331 / % possible obs: 88.3 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 42.9 Å2 / Rsym value: 0.036 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2.4→2.5 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.172 / % possible all: 60.3 |
Reflection | *PLUS Num. measured all: 99285 / Rmerge(I) obs: 0.036 |
Reflection shell | *PLUS % possible obs: 60.3 % / Rmerge(I) obs: 0.172 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ECF Resolution: 2.4→25 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: FREE R / σ(F): 0 Details: ADDITIONAL TOPOLOGY/PARAMETER FILES FOR THE CYS/ONL LINKAGE WERE USED, WHICH HAVE A NOMENCLATURE DIFFERENT FROM THE ONL RESIDUE IN THIS ENTRY.
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Displacement parameters | Biso mean: 34.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.35 |