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Yorodumi- PDB-1cli: X-RAY CRYSTAL STRUCTURE OF AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cli | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE (PURM), FROM THE E. COLI PURINE BIOSYNTHETIC PATHWAY, AT 2.5 A RESOLUTION | ||||||
Components | PROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE) | ||||||
Keywords | LIGASE / AIR SYNTHETASE / PURM / PURINE BIOSYNTHESIS / TRIFUNCTIONAL ENZYME / PURL / FGAR AMIDOTRANSFERASE / NOVEL FOLD | ||||||
Function / homology | Function and homology information phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / adenine biosynthetic process / phosphoribosylamine-glycine ligase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Li, C. / Kappock, T.J. / Stubbe, J. / Weaver, T.M. / Ealick, S.E. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 A resolution. Authors: Li, C. / Kappock, T.J. / Stubbe, J. / Weaver, T.M. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cli.cif.gz | 263 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cli.ent.gz | 211.9 KB | Display | PDB format |
PDBx/mmJSON format | 1cli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cli_validation.pdf.gz | 404.6 KB | Display | wwPDB validaton report |
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Full document | 1cli_full_validation.pdf.gz | 434.6 KB | Display | |
Data in XML | 1cli_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 1cli_validation.cif.gz | 46.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/1cli ftp://data.pdbj.org/pub/pdb/validation_reports/cl/1cli | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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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: (Code: given Matrix: (-0.6652, -0.2085, -0.717), Vector: |
-Components
#1: Protein | Mass: 36858.875 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: SULFATE BINDNG / Source: (gene. exp.) Escherichia coli (E. coli) / Description: CLONED GENE / Cellular location: CYTOPLASM / Gene: PURM / Plasmid: PJS119 / Species (production host): Escherichia coli / Cell (production host): BL21 / Cell line (production host): BL21 / Cellular location (production host): CYTOPLASM / Gene (production host): PURM / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P08178, phosphoribosylformylglycinamidine cyclo-ligase #2: Chemical | ChemComp-SO4 / #3: 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: 2.4 Å3/Da / Density % sol: 47.5 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 / Details: pH 5.6 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 170 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9792,0.9790,0.9638 | ||||||||||||
Detector | Type: ADSC / Detector: CCD / Date: Feb 1, 1998 / Details: MIRRORS | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→20 Å / Num. obs: 44742 / % possible obs: 91.4 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 35.7 Å2 / Rsym value: 4.7 / Net I/σ(I): 8.8 | ||||||||||||
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 5.1 / Rsym value: 14.3 / % possible all: 93 | ||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.047 | ||||||||||||
Reflection shell | *PLUS % possible obs: 93 % / Rmerge(I) obs: 0.143 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 16.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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