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- PDB-9em1: Human pyridoxal phosphatase in complex with 7,8-dihydroxyflavone ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9em1 | ||||||
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Title | Human pyridoxal phosphatase in complex with 7,8-dihydroxyflavone and phosphate | ||||||
![]() | Chronophin | ||||||
![]() | HYDROLASE / Inhibitor / PDXP / 7 8-dihydroxyflavone / Flavone / haloacid dehalogenase type hydrolases / HAD / phosphatase / Chronophin | ||||||
Function / homology | ![]() pyridoxal phosphatase / pyridoxal phosphate catabolic process / actin rod assembly / pyridoxal phosphatase activity / positive regulation of actin filament depolymerization / cellular response to ATP / regulation of mitotic nuclear division / myosin phosphatase activity / protein-serine/threonine phosphatase / dephosphorylation ...pyridoxal phosphatase / pyridoxal phosphate catabolic process / actin rod assembly / pyridoxal phosphatase activity / positive regulation of actin filament depolymerization / cellular response to ATP / regulation of mitotic nuclear division / myosin phosphatase activity / protein-serine/threonine phosphatase / dephosphorylation / phosphoprotein phosphatase activity / lamellipodium membrane / heat shock protein binding / protein dephosphorylation / regulation of cytokinesis / ruffle membrane / cell-cell junction / cytoskeleton / magnesium ion binding / protein homodimerization activity / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brenner, M. / Gohla, A. / Schindelin, H. | ||||||
Funding support | 1items
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![]() | ![]() Title: 7,8-Dihydroxyflavone is a direct inhibitor of human and murine pyridoxal phosphatase. Authors: Brenner, M. / Zink, C. / Witzinger, L. / Keller, A. / Hadamek, K. / Bothe, S. / Neuenschwander, M. / Villmann, C. / von Kries, J.P. / Schindelin, H. / Jeanclos, E. / Gohla, A. #1: ![]() Title: 7,8-Dihydroxyflavone is a direct inhibitor of pyridoxal phosphatase Authors: Brenner, M. / Zink, C. / Witzinger, L. / Keller, A. / Hadamek, K. / Bothe, S. / Neuenschwander, M. / Villmann, C. / von Kries, J.P. / Schindelin, H. / Jeanclos, E. / Gohla, A. #2: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / ![]() ![]() ![]() Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. #3: Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231.5 KB | Display | ![]() |
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PDB format | ![]() | 156 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8qfwC ![]() 8s8aC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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: 31738.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96GD0, protein-serine/threonine phosphatase, pyridoxal phosphatase |
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-Non-polymers , 5 types, 279 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / | ||
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#3: Chemical | ChemComp-UK9 / Mass: 254.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O4 / Feature type: SUBJECT OF INVESTIGATION | ||
#4: Chemical | ChemComp-GOL / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PDXP at 10 mg/ml in 50 mM Triethanolamine, 250 mM NaCl and 5 mM MgCl2 was crystallized against 0.1 M Tris pH 8.5, 1 M diammonium hydrogen phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 16, 2024 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873128 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→48.08 Å / Num. obs: 51537 / % possible obs: 100 % / Redundancy: 50.7 % / Biso Wilson estimate: 24.66 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.018 / Rrim(I) all: 0.127 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 51 % / Rmerge(I) obs: 4.893 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2467 / CC1/2: 0.526 / Rpim(I) all: 0.689 / Rrim(I) all: 4.942 / % possible all: 100 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→38.16 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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