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Yorodumi- PDB-1g4c: CRYSTAL STRUCTURE OF A COMPLEX OF HPPK(R92A) FROM E.COLI WITH MG2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g4c | ||||||
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Title | CRYSTAL STRUCTURE OF A COMPLEX OF HPPK(R92A) FROM E.COLI WITH MG2+ AT 1.65 ANGSTROM RESOLUTION | ||||||
Components | 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE | ||||||
Keywords | TRANSFERASE / PYROPHOSPHOKINASE / PYROPHOSPHORYL TRANSFER / FOLATE / HPPK / PTERIN / 6-HYDROXYMETHYL-7 / 8-DIHYDROPTERIN / ANTIMICROBIAL AGENT / DRUG DESIGN | ||||||
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 / phosphorylation / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Blaszczyk, J. / Ji, X. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Dynamic Roles of Arginine Residues 82 and 92 of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase: Crystallographic Studies Authors: BLASZCZYK, J. / Li, Y. / SHI, G. / YAN, H. / JI, X. #1: Journal: Structure / Year: 1999 Title: CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE, A POTENTIAL TARGET FOR THE DEVELOPMENT OF NOVEL ANTIMICROBIAL AGENTS Authors: XIAO, B. / SHI, G. / CHEN, X. / YAN, H. / JI, X. #2: Journal: Structure / Year: 2000 Title: CATALYTIC CENTER ASSEMBLY OF HPPK AS REVEALED BY THE CRYSTAL STRUCTURE OF A TERNARY COMPLEX AT 1.25 A RESOLUTION Authors: BLASZCZYK, J. / SHI, G. / YAN, H. / JI, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g4c.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g4c.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 1g4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/1g4c ftp://data.pdbj.org/pub/pdb/validation_reports/g4/1g4c | HTTPS FTP |
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-Related structure data
Related structure data | 1f9hC 1hq2C 1im6C 1kbrC 3ip0C 1hkaS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17880.418 Da / Num. of mol.: 2 / Mutation: R92A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET17B / Production host: Escherichia coli (E. coli) References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 1.92 Å3/Da / Density % sol: 33.4 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: PEG4000, MAGNESIUM CHLORIDE, TRIS-HCL, ACETATE, GLYCEROL, pH 8.40, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K | |||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.009 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2000 / Details: MIRROR |
Radiation | Monochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→40 Å / Num. all: 32443 / Num. obs: 32443 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.73 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.9123 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 2.431 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2 / Num. unique all: 3203 / % possible all: 98 |
Reflection | *PLUS Num. measured all: 88579 |
Reflection shell | *PLUS % possible obs: 98 % / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1HKA Resolution: 1.65→30 Å / Num. parameters: 10355 / Num. restraintsaints: 10586 / Cross valid method: FREE R / σ(F): 0 / 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 & KRETSINGER, J.MOL.BIOL. 91 (1975) 201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 4 / Occupancy sum hydrogen: 2476 / Occupancy sum non hydrogen: 2947 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.236 / Rfactor Rwork: 0.205 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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