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Yorodumi- PDB-1ecf: ESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ecf | ||||||
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Title | ESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMIDOTRANSFERASE | ||||||
Components | GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE | ||||||
Keywords | TRANSFERASE (GLUTAMINE AMIDOTRANSFERASE) / PURINE BIOSYNTHESIS / TRANSFERASE / GLYCOSYLTRANSFERASE / GLUTAMINE AMIDOTRANSFERASE | ||||||
Function / homology | Function and homology information amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / guanosine tetraphosphate binding / glutamine metabolic process / glycosyltransferase activity / magnesium ion binding / identical protein binding ...amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / guanosine tetraphosphate binding / glutamine metabolic process / glycosyltransferase activity / magnesium ion binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT, SIR PHASES FROM SEMET PROTEIN / Resolution: 2 Å | ||||||
Authors | Krahn, J.M. | ||||||
Citation | Journal: Protein Sci. / Year: 1998 Title: Crystal structure of glutamine phosphoribosylpyrophosphate amidotransferase from Escherichia coli. Authors: Muchmore, C.R. / Krahn, J.M. / Kim, J.H. / Zalkin, H. / Smith, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ecf.cif.gz | 229.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ecf.ent.gz | 186.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ecf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ecf_validation.pdf.gz | 602.8 KB | Display | wwPDB validaton report |
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Full document | 1ecf_full_validation.pdf.gz | 603.3 KB | Display | |
Data in XML | 1ecf_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 1ecf_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/1ecf ftp://data.pdbj.org/pub/pdb/validation_reports/ec/1ecf | HTTPS FTP |
-Related structure data
Related structure data | 1ecjC 1gphS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.0809, -0.0094, 0.9967), Vector: Details | PHE B 88 - SER B 92 EXISTS IN TWO DISTINCT CONFORMATIONS AS A RESULT OF THE BINDING OF PIPES BUFFER ALONG THE CRYSTALLOGRAPHIC MOLECULAR TWO-FOLD AXIS, AND IS THEREFORE POORLY DEFINED. APPLICATION OF THE CRYSTALLOGRAPHIC SYMMETRY OPERATOR TO THE SECOND SET OF RESIDUES WILL GENERATE A COMPLETE ASYMMETRIC MODEL OF THIS SITE. | |
-Components
#1: Protein | Mass: 56422.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Description: T7 PHI10 PROMOTER / Cell line: BL21 / Gene: PURF / Plasmid: PT7F1 / Species (production host): Escherichia coli / Gene (production host): PURF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P00496, UniProt: P0AG16*PLUS, amidophosphoribosyltransferase #2: Chemical | ChemComp-PIN / #3: Water | ChemComp-HOH / | Compound details | GLU A 303 AND GLU B 303 ARE CIS-GLUTAMINE - PART OF A PHOSPHATE BINDING SITE INVOLVED IN BINDING ...GLU A 303 AND GLU B 303 ARE CIS-GLUTAMINE - PART OF A PHOSPHATE BINDING SITE INVOLVED IN BINDING BOTH SUBSTRATE AND INHIBITORS | |
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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: 2.17 Å3/Da / Density % sol: 40 % Description: ORIGINAL MOLECULAR REPLACEMENT SOLUTION WAS OBTAINED IN A DIFFERENT CRYSTAL FORM. | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 / Details: pH 5.6 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 18, 1995 |
Radiation | Monochromator: MSC DOUBLE MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 65480 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 4.5 / % possible all: 92.7 |
Reflection | *PLUS Num. measured all: 268969 |
Reflection shell | *PLUS % possible obs: 92.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT, SIR PHASES FROM SEMET PROTEIN Starting model: 1GPH Resolution: 2→30 Å / σ(F): 0 Details: TYR 94 IN EACH CHAIN HAS PHI/PSI VALUES THAT ARE NORMALLY DISALLOWED. IT FORMS A SHARP BETA-TURN WITH PRO 93, A CIS-PROLINE. THE DISTANCE BETWEEN X982 AND X230 IS ARTIFICIALLY SHORT DUE TO ...Details: TYR 94 IN EACH CHAIN HAS PHI/PSI VALUES THAT ARE NORMALLY DISALLOWED. IT FORMS A SHARP BETA-TURN WITH PRO 93, A CIS-PROLINE. THE DISTANCE BETWEEN X982 AND X230 IS ARTIFICIALLY SHORT DUE TO UNMODELLED HETEROGENEITY AT A SPECIAL POSITION NEAR X230. ADDITIONAL UNMODELED ELECTRON DENSITY IS PRESENT NEAR THE CYS 1 SULFUR. IT APPEARS TO REPRESENT A HETEROGENEOUS OXIDATION BY OXYGEN AND SULFUR COMPOUNDS.
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Displacement parameters | Biso mean: 24.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 65453 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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