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- PDB-1ecc: ESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMI... -
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Open data
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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 | ||||||
![]() | GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE | ||||||
![]() | TRANSFERASE / GLUTAMINE AMIDOTRANSFERASE / PURINE BIOSYNTHESIS / GLYCOSYLTRANSFERASE | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Krahn, J.M. / Smith, J.L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 206.8 KB | Display | ![]() |
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PDB format | ![]() | 168.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 527 KB | Display | ![]() |
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Full document | ![]() | 533.8 KB | Display | |
Data in XML | ![]() | 24.4 KB | Display | |
Data in CIF | ![]() | 37.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ecbC ![]() 1ecfS 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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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: |
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Components
#1: Protein | Mass: 56422.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() 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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.35 |