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Yorodumi- PDB-1dqp: CRYSTAL STRUCTURE OF GIARDIA GUANINE PHOSPHORIBOSYLTRANSFERASE CO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dqp | ||||||
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Title | CRYSTAL STRUCTURE OF GIARDIA GUANINE PHOSPHORIBOSYLTRANSFERASE COMPLEXED WITH IMMUCILLING | ||||||
Components | GUANINE PHOSPHORIBOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / protein-inhibitor complex / immucillinG / 9-deazaguanine | ||||||
Function / homology | Function and homology information guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / nucleotide binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Giardia intestinalis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å | ||||||
Authors | Shi, W. / Munagala, N.R. / Wang, C.C. / Li, C.M. / Tyler, P.C. / Furneaux, R.H. / Grubmeyer, C. / Schramm, V.L. / Almo, S.C. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Crystal structures of Giardia lamblia guanine phosphoribosyltransferase at 1.75 A(,). Authors: Shi, W. / Munagala, N.R. / Wang, C.C. / Li, C.M. / Tyler, P.C. / Furneaux, R.H. / Grubmeyer, C. / Schramm, V.L. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dqp.cif.gz | 113.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dqp.ent.gz | 88.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dqp_validation.pdf.gz | 482.2 KB | Display | wwPDB validaton report |
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Full document | 1dqp_full_validation.pdf.gz | 488.9 KB | Display | |
Data in XML | 1dqp_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 1dqp_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/1dqp ftp://data.pdbj.org/pub/pdb/validation_reports/dq/1dqp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 26367.279 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Giardia intestinalis (eukaryote) / Production host: Escherichia coli (E. coli) References: UniProt: Q24973, hypoxanthine phosphoribosyltransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | 9-deazaguanine is the only part of immucillinG ligand that could be seen in the density. Because ...9-deazaguanine is the only part of immucillinG ligand that could be seen in the density. Because immucillinG lacks a 5'-phosphate group, the sugar part of the ligand is not well ordered in this structure. | |
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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: 2.36 Å3/Da / Density % sol: 47.92 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% polyethylene glycol 4000, 5% isopropanol, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.979 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 22, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. all: 50590 / Num. obs: 50590 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.039 / Net I/σ(I): 40.8 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 3.6 % / Num. unique all: 2485 / Rsym value: 0.075 / % possible all: 98.7 |
Reflection | *PLUS Num. measured all: 210690 / Rmerge(I) obs: 0.039 |
Reflection shell | *PLUS % possible obs: 98.7 % / Rmerge(I) obs: 0.075 |
-Processing
Software |
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Refinement | Resolution: 1.75→20 Å / σ(F): 2 / σ(I): 1.4 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
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Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 45122 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |