+Open data
-Basic information
Entry | Database: PDB / ID: 1h3d | ||||||
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Title | STRUCTURE OF THE E.COLI ATP-PHOSPHORIBOSYLTRANSFERASE | ||||||
Components | ATP-PHOSPHORIBOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / PHOSPHORIBOSYLTRANSFERASE / HISITIDINE BIOSYNTHESIS / GLYCOSYLTRANSFERASE | ||||||
Function / homology | Function and homology information ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / histidine biosynthetic process / magnesium ion binding / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Lohkamp, B. / McDermott, G. / Coggins, J.R. / Lapthorn, A.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: The Structure of Escherichia Coli ATP-Phosphoribosyltransferase: Identification of Substrate Binding Sites and Mode of AMP Inhibition Authors: Lohkamp, B. / Mcdermott, G. / Campbell, S. / Coggins, J.R. / Lapthorn, A.J. | ||||||
History |
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Remark 285 | TEXT TO EXPLAIN UNUSUAL UNIT-CELL DATA: HEXAGONAL SETTING USED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h3d.cif.gz | 62.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h3d.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 1h3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/1h3d ftp://data.pdbj.org/pub/pdb/validation_reports/h3/1h3d | HTTPS FTP |
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-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: 33408.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PTB361 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS References: UniProt: P10366, UniProt: P60757*PLUS, ATP phosphoribosyltransferase | ||
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#2: Chemical | ChemComp-AMP / | ||
#3: Chemical | Compound details | CATALYTIC ACTIVITY: 1-(5-PHOSPHO-D-RIBOSYL)-ATP + DIPHOSPHATE = ATP + 5-PHOSPHO-ALPHA-D-RIBOSE 1- ...CATALYTIC ACTIVITY: 1-(5-PHOSPHO-D-RIBOSYL)-ATP + DIPHOSPHAT | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 Details: PROTEIN WAS CRYSTALLIZED FROM 1.3M SODIUM TARTRATE, 50-200MM MGCL2, 100MM CITRATE BUFFER, PH 5.6, IN PRESENCE OF 2MM AMP | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 5.6 / Method: vapor diffusion, sitting drop / Details: Lohkamp, B., (2000) Acta Crystallogr., D56, 1488. | ||||||||||||||||||||||||||||||||||||||||||
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: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→81.65 Å / Num. obs: 10860 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 83.842 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.7 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→81.65 Å / SU B: 13.292 / SU ML: 0.2812 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.89567 / ESU R Free: 0.36452
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Displacement parameters | Biso mean: 46.118 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→81.65 Å
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Refinement | *PLUS Highest resolution: 2.7 Å / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.222 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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