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- PDB-1ecb: ESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ecb | ||||||
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Title | ESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMIDOTRANSFERASE COMPLEXED WITH 2 GMP, 1 MG PER SUBUNIT | ||||||
![]() | GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE | ||||||
![]() | TRANSFERASE / GLUTAMINE AMIDOTRANSFERASE / PURINE BIOSYNTHESIS / GLYCOSYLTRANSFERASE / GMP / GUANINE 5'-MONOPHOSPHATE | ||||||
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 | ![]() | 377.8 KB | Display | ![]() |
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PDB format | ![]() | 308.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 757.3 KB | Display | ![]() |
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Full document | ![]() | 803.3 KB | Display | |
Data in XML | ![]() | 43.3 KB | Display | |
Data in CIF | ![]() | 63 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1eccC ![]() 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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2 | ![]()
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3 |
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4 | ![]()
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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.) ![]() ![]() ![]() ![]() References: UniProt: P00496, UniProt: P0AG16*PLUS, amidophosphoribosyltransferase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-5GP / #4: Water | ChemComp-HOH / | Compound details | THE GUANINE BASE OF GMP BOUND IN THE PRTASE ACTIVE SITE IS NOT WELL ORDERED, AND APPEARS TO WOBBLE ...THE GUANINE BASE OF GMP BOUND IN THE PRTASE ACTIVE SITE IS NOT WELL ORDERED, AND APPEARS TO WOBBLE IN THE PLANE OF THE BASE. ONLY A SINGLE CONFORMER HAS BEEN INCLUDED IN THIS MODEL TO THE LIMITED RESOLUTION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 5 MM GMP, 20 MM MGCL2, 100 MM BIS-TRIS PH 6.0, 10% PEG-3350, 10% 2-PROPANOL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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 / Detector: IMAGE PLATE / Date: Mar 1, 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: 2.7→30 Å / Num. obs: 58955 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rsym value: 0.092 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.33 / % possible all: 78.9 |
Reflection | *PLUS Num. measured all: 354923 / Rmerge(I) obs: 0.092 |
Reflection shell | *PLUS % possible obs: 78.9 % / Rmerge(I) obs: 0.33 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ECF Resolution: 2.7→15 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: 2.7→15 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: 2.7→2.8 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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