+Open data
-Basic information
Entry | Database: PDB / ID: 1b6r | ||||||
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Title | N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE FROM E. COLI | ||||||
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 / MIR / Resolution: 2.1 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 | 1b6r.cif.gz | 81.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b6r.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 1b6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b6r_validation.pdf.gz | 379.1 KB | Display | wwPDB validaton report |
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Full document | 1b6r_full_validation.pdf.gz | 396.3 KB | Display | |
Data in XML | 1b6r_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 1b6r_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/1b6r ftp://data.pdbj.org/pub/pdb/validation_reports/b6/1b6r | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39528.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) References: UniProt: P09029, phosphoribosylaminoimidazole carboxylase |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 64 % | ||||||||||||||||||||
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Crystal grow | pH: 7.8 / Details: 100MM HEPPS, PH 7.8 0.575 M AMMONIUM SULFATE | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: macroseeding | ||||||||||||||||||||
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 / Detector: AREA DETECTOR / Date: Feb 15, 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: 2.1→30 Å / Num. obs: 30332 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.292 / % possible all: 78.9 |
Reflection shell | *PLUS % possible obs: 78.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.1→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: TNT / Bsol: 696.7 Å2 / ksol: 1.032 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5D / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.196 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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