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- PDB-1l1q: Crystal Structure of APRTase from Giardia lamblia Complexed with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1l1q | ||||||
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Title | Crystal Structure of APRTase from Giardia lamblia Complexed with 9-deazaadenine | ||||||
![]() | Adenine phosphoribosyltransferase | ||||||
![]() | TRANSFERASE / adenine / APRTase / Giardia lamblia / purine metabolism / catalytic loop | ||||||
Function / homology | ![]() adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shi, W. / Sarver, A.E. / Wang, C.C. / Tanaka, K.S. / Almo, S.C. / Schramm, V.L. | ||||||
![]() | ![]() Title: Closed Site Complexes of Adenine Phosphoribosyltransferase from Giardia lamblia Reveal a Mechanism of Ribosyl Migration. Authors: Shi, W. / Sarver, A.E. / Wang, C.C. / Tanaka, K.S. / Almo, S.C. / Schramm, V.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 | ![]() | 49.6 KB | Display | ![]() |
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PDB format | ![]() | 34.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1l1rC ![]() 1g2pS C: citing same article ( S: Starting model for refinement |
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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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Components on special symmetry positions |
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Details | The biological assembly is a dimer generated from the monomer in the asymmetric unit by applying the crystallographic 2-fold. |
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Components
#1: Protein | Mass: 20290.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q967M2, adenine phosphoribosyltransferase | ||||
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#2: Chemical | #3: Chemical | ChemComp-9DA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, ammonium sulfate, urea, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 29, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→25 Å / Num. all: 16337 / Num. obs: 16337 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 15.4 Å2 / Rsym value: 0.027 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1602 / Rsym value: 0.352 / % possible all: 98.8 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 73591 / Rmerge(I) obs: 0.027 |
Reflection shell | *PLUS % possible obs: 98.8 % / Rmerge(I) obs: 0.352 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1G2P Resolution: 1.85→25 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: flat model / Bsol: 47.1677 Å2 / ksol: 0.369266 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Refinement | *PLUS Lowest resolution: 25 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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