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Yorodumi- PDB-1gph: STRUCTURE OF THE ALLOSTERIC REGULATORY ENZYME OF PURINE BIOSYNTHESIS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gph | ||||||
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Title | STRUCTURE OF THE ALLOSTERIC REGULATORY ENZYME OF PURINE BIOSYNTHESIS | ||||||
Components | GLUTAMINE PHOSPHORIBOSYL-PYROPHOSPHATE AMIDOTRANSFERASE | ||||||
Keywords | TRANSFERASE / GLUTAMINE AMIDOTRANSFERASE | ||||||
Function / homology | Function and homology information amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / glutamine metabolic process / 4 iron, 4 sulfur cluster binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | ||||||
Authors | Smith, J.L. | ||||||
Citation | Journal: Science / Year: 1994 Title: Structure of the allosteric regulatory enzyme of purine biosynthesis. Authors: Smith, J.L. / Zaluzec, E.J. / Wery, J.P. / Niu, L. / Switzer, R.L. / Zalkin, H. / Satow, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gph.cif.gz | 331.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gph.ent.gz | 274.8 KB | Display | PDB format |
PDBx/mmJSON format | 1gph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gph_validation.pdf.gz | 765.1 KB | Display | wwPDB validaton report |
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Full document | 1gph_full_validation.pdf.gz | 819.4 KB | Display | |
Data in XML | 1gph_validation.xml.gz | 42.3 KB | Display | |
Data in CIF | 1gph_validation.cif.gz | 62 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/1gph ftp://data.pdbj.org/pub/pdb/validation_reports/gp/1gph | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 1 86 / 2: CIS PROLINE - PRO 2 86 / 3: CIS PROLINE - PRO 3 86 / 4: CIS PROLINE - PRO 4 86 | ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 50507.203 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / References: UniProt: P00497, amidophosphoribosyltransferase #2: Chemical | ChemComp-SF4 / #3: Chemical | ChemComp-AMP / Nonpolymer details | THE FE ATOMS OF THE [4FE-4S] CLUSTER ARE LIGATED BY CYSTEINE S(GAMMA) ATOMS AS FOLLOWS: FE 1 - SG ...THE FE ATOMS OF THE [4FE-4S] CLUSTER ARE LIGATED BY CYSTEINE S(GAMMA) ATOMS AS FOLLOWS: FE 1 - SG CYS 437; FE 2 - SG CYS 236; FE 3 - SG CYS 440; FE 4 - SG CYS 382. THE AMP MOLECULE THAT IS RESIDUE 467 IS BOUND TO THE SITE WHERE THE SUBSTRATE PRPP IS PRESUMED TO BIND. THE AMP MOLECULE THAT IS RESIDUE 468 IS BOUND BETWEEN SUBUNITS IN WHAT IS PRESUMED TO BE AN ALLOSTERIC | Sequence details | THE STRUCTURE DIFFERS FROM THE DEPOSITED SEQUENCE IN TWO PLACES: 1) AN 11-RESIDUE PROPEPTIDE ...THE STRUCTURE DIFFERS FROM THE DEPOSITED SEQUENCE IN TWO PLACES: 1) AN 11-RESIDUE PROPEPTIDE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.04 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.9 / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 3 Å / Num. obs: 41267 / % possible obs: 90.1 % |
-Processing
Software |
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Refinement | Resolution: 3→7 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 3→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.182 / Rfactor Rwork: 0.182 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.3 |