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Yorodumi- PDB-3kuh: Crystal structure of E. coli HPPK(H115A) in complex with AMPCPP and HP -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kuh | ||||||
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Title | Crystal structure of E. coli HPPK(H115A) in complex with AMPCPP and HP | ||||||
Components | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase | ||||||
Keywords | TRANSFERASE / alpha beta / ATP-binding / Folate biosynthesis / Kinase / Nucleotide-binding | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.35 Å | ||||||
Authors | Blaszczyk, J. / Li, Y. / Yan, H. / Ji, X. | ||||||
Citation | Journal: To be Published Title: Roles of residues E77 and H115 in E. coli HPPK Authors: Li, Y. / Blaszczyk, J. / Ji, X. / Yan, H. #1: 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 | 3kuh.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kuh.ent.gz | 71.8 KB | Display | PDB format |
PDBx/mmJSON format | 3kuh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/3kuh ftp://data.pdbj.org/pub/pdb/validation_reports/ku/3kuh | HTTPS FTP |
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-Related structure data
Related structure data | 3kueC 3kugC 1q0nS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17899.465 Da / Num. of mol.: 1 / Mutation: H116A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0142, foIK, folK, JW0138 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase |
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-Non-polymers , 6 types, 352 molecules
#2: Chemical | ChemComp-APC / | ||||||
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#3: Chemical | ChemComp-PH2 / | ||||||
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-ACT / | #7: 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: 2.04 Å3/Da / Density % sol: 39.66 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, Sodium acetate, Ammonium acetate, glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.05517 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2000 / Details: mirrors |
Radiation | Monochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05517 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. all: 31767 / Num. obs: 31767 / % possible obs: 99.8 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 0.101 Å2 / Rmerge(I) obs: 0.089 / Χ2: 1.002 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3149 / Χ2: 0.994 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1Q0N Resolution: 1.35→27.12 Å / Occupancy max: 1 / Occupancy min: 0.14 / SU ML: 0.15 Isotropic thermal model: Anisotropic for fully occupied non-hydrogen atoms Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: ML Details: The structure was refined for a total of 25 cycles, including 5 cycles with CNS, 10 cycles with SHELXL, and 10 cycles with PHENIX
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.97 Å2 / ksol: 0.343 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.55 Å2 / Biso mean: 13.499 Å2 / Biso min: 0.89 Å2
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Refine analyze | Luzzati coordinate error obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→27.12 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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