+Open data
-Basic information
Entry | Database: PDB / ID: 1hka | ||||||
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Title | 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE | ||||||
Components | 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE | ||||||
Keywords | TRANSFERASE / PYROPHOSPHORYL TRANSFER / PYROPHOSPHOKINASE / KINASE / FOLATE / 6-HYDROXYMETHYL-7 / 8-DIHYDROPTERIN | ||||||
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 / MAD / Resolution: 1.5 Å | ||||||
Authors | Xiao, B. / Shi, G. / Chen, X. / Yan, H. / Ji, X. | ||||||
Citation | Journal: Structure Fold.Des. / 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. #1: Journal: J.Bacteriol. / Year: 1992 Title: Cloning, Sequence Analysis, and Overexpression of Escherichia Coli Folk, the Gene Coding for 7,8-Dihydro-6-Hydroxymethylpterin-Pyrophosphokinase Authors: Talarico, T.L. / Ray, P.H. / Dev, I.K. / Merrill, B.M. / Dallas, W.S. #2: Journal: J.Bacteriol. / Year: 1991 Title: Purification and Partial Characterization of 7,8-Dihydro-6-Hydroxymethylpterin-Pyrophosphokinase and 7,8-Dihydropteroate Synthase from Escherichia Coli Mc4100 Authors: Talarico, T.L. / Dev, I.K. / Dallas, W.S. / Ferone, R. / Ray, P.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hka.cif.gz | 50.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hka.ent.gz | 35.3 KB | Display | PDB format |
PDBx/mmJSON format | 1hka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hka_validation.pdf.gz | 365.1 KB | Display | wwPDB validaton report |
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Full document | 1hka_full_validation.pdf.gz | 366.4 KB | Display | |
Data in XML | 1hka_validation.xml.gz | 5 KB | Display | |
Data in CIF | 1hka_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/1hka ftp://data.pdbj.org/pub/pdb/validation_reports/hk/1hka | HTTPS FTP |
-Related structure data
Similar structure data |
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-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) / Gene: FOLK / Production host: Escherichia coli (E. coli) References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase |
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#2: 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: 1.66 Å3/Da / Density % sol: 26 % | ||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9686, 0.9788, 0.9792, 0.9870 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 20, 1997 / Details: MIRROR | |||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→20 Å / Num. obs: 23352 / % possible obs: 95.8 % / Observed criterion σ(I): -0.5 / Redundancy: 5.65 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.4 | |||||||||||||||
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.81 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.06 / % possible all: 89.9 | |||||||||||||||
Reflection | *PLUS Num. measured all: 132018 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 89.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→20 Å / Num. parameters: 6235 / Num. restraintsaints: 5591 / Cross valid method: FREE R IN FIRST STAGE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI AND HOPE, J.APPL.CRYST. 28 (1995)53-56
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1503 | |||||||||||||||||||||||||||||||||
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(I): 2 / Rfactor all: 0.182 / Rfactor obs: 0.174 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |