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Yorodumi- PDB-1eqm: CRYSTAL STRUCTURE OF BINARY COMPLEX OF 6-HYDROXYMETHYL-7,8-DIHYDR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eqm | ||||||
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Title | CRYSTAL STRUCTURE OF BINARY COMPLEX OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE WITH ADENOSINE-5'-DIPHOSPHATE | ||||||
Components | 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE | ||||||
Keywords | TRANSFERASE / PYROPHOSPHOKINASE / PYROPHOSPHORYL TRANSFER / FOLATE / HPPK / PTERIN / ANTIMICROBIAL AGENT / DRUG DESIGN / SUBSTRATE SPECIFICITY | ||||||
Function / homology | Function and homology information 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Xiao, B. / Blaszczyk, J. / Ji, X. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Unusual conformational changes in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as revealed by X-ray crystallography and NMR. Authors: Xiao, B. / Shi, G. / Gao, J. / Blaszczyk, J. / Liu, Q. / Ji, X. / Yan, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eqm.cif.gz | 55.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eqm.ent.gz | 37.5 KB | Display | PDB format |
PDBx/mmJSON format | 1eqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eqm_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1eqm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1eqm_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 1eqm_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/1eqm ftp://data.pdbj.org/pub/pdb/validation_reports/eq/1eqm | HTTPS FTP |
-Related structure data
Related structure data | 1eq0C 1hkaS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 17966.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-ADP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 26.4 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, Tris-HCl, acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18-20 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X9B / Wavelength: 0.992 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 23, 1998 / Details: MIRROR |
Radiation | Monochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.992 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. all: 23029 / Num. obs: 23029 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 1.97 / Num. unique all: 2003 / % possible all: 85.4 |
Reflection | *PLUS Num. measured all: 83381 |
Reflection shell | *PLUS % possible obs: 85.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HKA Resolution: 1.5→20 Å / Num. parameters: 6411 / Num. restraintsaints: 5634 / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER Details: Least-squares refinement using the Konnert-Hendrickson conjugate-gradient algorithm
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Solvent computation | Solvent model: Moews and Kretsinger, J.Mol.Biol. 91(1973)201-202 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1523 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 4 / % reflection Rfree: 5.083 % | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |