+Open data
-Basic information
Entry | Database: PDB / ID: 3hcx | ||||||
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Title | Crystal structure of E. coli HPPK(N10A) | ||||||
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 K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å | ||||||
Authors | Blaszczyk, J. / Li, Y. / Yan, H. / Ji, X. | ||||||
Citation | Journal: To be Published Title: Role of loop coupling in enzymatic catalysis and conformational dynamics Authors: Blaszczyk, J. / Li, Y. / 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 | 3hcx.cif.gz | 50.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hcx.ent.gz | 35 KB | Display | PDB format |
PDBx/mmJSON format | 3hcx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/3hcx ftp://data.pdbj.org/pub/pdb/validation_reports/hc/3hcx | HTTPS FTP |
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-Related structure data
Related structure data | 3hd1C 3hd2C 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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Unit cell |
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-Components
#1: Protein | Mass: 17923.510 Da / Num. of mol.: 1 / Mutation: N10A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / 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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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-TRS / |
#4: 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: 2.05 Å3/Da / Density % sol: 39.92 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, Sodium acetate, Glycerol, Tris-HCl, pH 8.5, 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: 0.917 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 1999 / Details: mirrors |
Radiation | Monochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.917 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. all: 14669 / Num. obs: 14669 / % possible obs: 99.8 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.047 / Χ2: 1 / Net I/σ(I): 24.571 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 1.92 / Num. unique all: 1471 / Χ2: 0.997 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1HKA Resolution: 1.75→19.524 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.846 / SU ML: 0.27 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML Details: The structure was refined for a total of 24 cycles, including 8 cycles with CNS, 7 cycles with SHELX, and 9 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: 61.825 Å2 / ksol: 0.354 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.68 Å2 / Biso mean: 29.043 Å2 / Biso min: 13.68 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→19.524 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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