+Open data
-Basic information
Entry | Database: PDB / ID: 1b6s | ||||||
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Title | STRUCTURE OF N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE | ||||||
Components | PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE) | ||||||
Keywords | LYASE / ATP-GRASP / CARBOXYPHOSPHATE / PURINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information 5-(carboxyamino)imidazole ribonucleotide synthase / 5-(carboxyamino)imidazole ribonucleotide synthase activity / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Thoden, J.B. / Kappock, T.J. / Stubbe, J. / Holden, H.M. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Three-dimensional structure of N5-carboxyaminoimidazole ribonucleotide synthetase: a member of the ATP grasp protein superfamily. Authors: Thoden, J.B. / Kappock, T.J. / Stubbe, J. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b6s.cif.gz | 295.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b6s.ent.gz | 236.3 KB | Display | PDB format |
PDBx/mmJSON format | 1b6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/1b6s ftp://data.pdbj.org/pub/pdb/validation_reports/b6/1b6s | HTTPS FTP |
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-Related structure data
Related structure data | 1b6rSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39528.988 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) References: UniProt: P09029, phosphoribosylaminoimidazole carboxylase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ADP / #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: 3.3 Å3/Da / Density % sol: 62 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: BRUKER AXS / Detector: AREA DETECTOR / Date: Oct 1, 1998 / Details: GOBEL MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 66345 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.072 / Rsym value: 0.72 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.5→2.61 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.181 / % possible all: 89.6 |
Reflection shell | *PLUS % possible obs: 89.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B6R Resolution: 2.5→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: TNT / Bsol: 282.7 Å2 / ksol: 0.915 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5D / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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