+Open data
-Basic information
Entry | Database: PDB / ID: 1pkx | ||||||
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Title | Crystal Structure of human ATIC in complex with XMP | ||||||
Components | Bifunctional purine biosynthesis protein PURH | ||||||
Keywords | TRANSFERASE / HYDROLASE / ATIC / AICAR transformylase / IMP Cyclohydrolase / xanthosine monophosphate / purine biosynthesis | ||||||
Function / homology | Function and homology information phosphoribosylaminoimidazolecarboxamide formyltransferase / phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase / IMP cyclohydrolase activity / 'de novo' XMP biosynthetic process / brainstem development / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / GMP biosynthetic process / cellular response to interleukin-7 ...phosphoribosylaminoimidazolecarboxamide formyltransferase / phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase / IMP cyclohydrolase activity / 'de novo' XMP biosynthetic process / brainstem development / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / GMP biosynthetic process / cellular response to interleukin-7 / nucleobase-containing compound metabolic process / 'de novo' IMP biosynthetic process / dihydrofolate metabolic process / : / animal organ regeneration / tetrahydrofolate biosynthetic process / cerebellum development / cerebral cortex development / Signaling by ALK fusions and activated point mutants / cadherin binding / protein homodimerization activity / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wolan, D.W. / Cheong, C.G. / Greasley, S.E. / Wilson, I.A. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Structural Insights into the Human and Avian IMP Cyclohydrolase Mechanism via Crystal Structures with the Bound XMP Inhibitor. Authors: Wolan, D.W. / Cheong, C.G. / Greasley, S.E. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pkx.cif.gz | 465.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pkx.ent.gz | 376.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pkx_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1pkx_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1pkx_validation.xml.gz | 90.2 KB | Display | |
Data in CIF | 1pkx_validation.cif.gz | 129 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/1pkx ftp://data.pdbj.org/pub/pdb/validation_reports/pk/1pkx | HTTPS FTP |
-Related structure data
Related structure data | 1g8mS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | biological unit is a homodimer and AU contains two dimers |
-Components
#1: Protein | Mass: 64693.719 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Includes: Phosphoribosylaminoimidazolecarboxamide formyltransferase (AICAR transformylase) and IMP cyclohydrolase (Inosinicase) (IMP synthetase) Source: (gene. exp.) Homo sapiens (human) / Gene: ATIC / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner DE3 References: UniProt: P31939, phosphoribosylaminoimidazolecarboxamide formyltransferase, IMP cyclohydrolase #2: Chemical | ChemComp-K / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.52 Å3/Da / Density % sol: 51.18 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: Polyethylene glycol 3000, pH 7.5-8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, sitting drop / PH range low: 8 / PH range high: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL9-2 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 177135 / % possible obs: 87.7 % / Redundancy: 2.1 % / Rsym value: 0.053 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.394 / % possible all: 47.8 |
Reflection | *PLUS Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS % possible obs: 47.8 % / Num. unique obs: 9598 / Rmerge(I) obs: 0.394 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1G8M Resolution: 1.9→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5.2 % | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |