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- PDB-8s8a: Human pyridoxal phosphatase in complex with 7,8-dihydroxyflavone ... -

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Basic information

Entry
Database: PDB / ID: 8s8a
TitleHuman pyridoxal phosphatase in complex with 7,8-dihydroxyflavone without phosphate
ComponentsChronophin
KeywordsHYDROLASE / Inhibitor / PDXP / 7 8-dihydroxyflavone / Flavone / Chronophin
Function / homology
Function and homology information


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 / phosphoprotein phosphatase activity ...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 / phosphoprotein phosphatase activity / lamellipodium membrane / dephosphorylation / heat shock protein binding / protein dephosphorylation / regulation of cytokinesis / ruffle membrane / cell-cell junction / cytoskeleton / magnesium ion binding / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
2-phosphoglycolate phosphatase, eukaryotic / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
FORMIC ACID / : / Chronophin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBrenner, M. / Gohla, A. / Schindelin, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Elife / Year: 2024
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: Journal: Elife / Year: 2024
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.,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.
#3: 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.
History
DepositionMar 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Revision 1.2Jun 26, 2024Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chronophin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0985
Polymers31,7381
Non-polymers3604
Water4,864270
1
A: Chronophin
hetero molecules

A: Chronophin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,19610
Polymers63,4762
Non-polymers7208
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2850 Å2
ΔGint-57 kcal/mol
Surface area24620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.037, 54.037, 212.493
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-667-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Chronophin / Pyridoxal phosphate phosphatase / PLP phosphatase


Mass: 31738.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDXP, CIN, PLP, PLPP / Production host: Escherichia coli (E. coli)
References: UniProt: Q96GD0, protein-serine/threonine phosphatase, pyridoxal phosphatase

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Non-polymers , 5 types, 274 molecules

#2: Chemical ChemComp-UK9 / 7,8-bis(oxidanyl)-2-phenyl-chromen-4-one


Mass: 254.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PDXP at 10 mg/ml in 50 mM Triethanolamine, 250 mM NaCl and 5 mM MgCl2 was crystallized against 0.1 M HEPES, 15 % Tacsimate, 2 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 16, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.5→48.17 Å / Num. obs: 51834 / % possible obs: 100 % / Redundancy: 25.6 % / Biso Wilson estimate: 28.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.017 / Rrim(I) all: 0.083 / Net I/σ(I): 17.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 26 % / Rmerge(I) obs: 3.67 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2480 / CC1/2: 0.579 / Rpim(I) all: 0.731 / Rrim(I) all: 3.743 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→48.17 Å / SU ML: 0.1944 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2262
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.205 2477 4.79 %
Rwork0.1817 49215 -
obs0.1829 51692 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.21 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2207 0 24 270 2501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00482543
X-RAY DIFFRACTIONf_angle_d0.80283492
X-RAY DIFFRACTIONf_chiral_restr0.046381
X-RAY DIFFRACTIONf_plane_restr0.0103485
X-RAY DIFFRACTIONf_dihedral_angle_d12.66461009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.29541220.30262672X-RAY DIFFRACTION99.89
1.53-1.560.29861390.28212649X-RAY DIFFRACTION99.93
1.56-1.590.31791470.2942684X-RAY DIFFRACTION99.86
1.59-1.630.31741210.3052695X-RAY DIFFRACTION99.93
1.63-1.670.32661460.26942649X-RAY DIFFRACTION99.89
1.67-1.720.23741310.22392673X-RAY DIFFRACTION99.89
1.72-1.770.1881240.19512722X-RAY DIFFRACTION99.96
1.77-1.820.22271450.19362697X-RAY DIFFRACTION99.93
1.82-1.890.22061300.19152710X-RAY DIFFRACTION99.96
1.89-1.970.22871500.18972695X-RAY DIFFRACTION100
1.97-2.060.19311490.17612705X-RAY DIFFRACTION100
2.06-2.160.19641240.1722769X-RAY DIFFRACTION99.97
2.16-2.30.19431260.16692710X-RAY DIFFRACTION100
2.3-2.480.20591510.16732754X-RAY DIFFRACTION100
2.48-2.730.19911160.17422800X-RAY DIFFRACTION100
2.73-3.120.19651410.17892763X-RAY DIFFRACTION99.97
3.12-3.930.19481510.16522840X-RAY DIFFRACTION100
3.93-48.170.19891640.18223028X-RAY DIFFRACTION99.97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.283660543760.733371626887-0.1660640966851.945958922310.2526712192450.9309476712-0.02931716395160.148779851004-0.0633323994872-0.219710810950.04720049817140.1503197394150.002858801696550.00625507347344-1.34605544737E-50.397019639609-0.00991630901321-0.01880828547620.1916385201820.01092105270170.24156892089-4.84111531264-3.3132068825822.1275138983
21.38764985645-0.593324126408-0.2041465603180.3257585002650.02731196817180.570129812691-0.02073991883740.2870719568-0.117324635171-0.215705986526-0.032550235403-0.08518366408-0.09124394833820.306397784738-0.08218065289660.403187257144-0.002805713576330.08352305324760.2304741117660.01670197726750.29751956768515.6636049834-0.60723905918332.5523662706
30.468676696433-0.346174688668-0.08967611139210.291590183545-0.04126952166520.294179341261-0.0146783038442-0.03066650845760.0133516185753-0.212315891508-0.0284999833505-0.2827998958630.06286841587760.227869040367-1.09535164166E-50.301597913207-0.01464313683980.06395242505950.2819678462610.0152515676930.33882780754222.7427706745-1.0995312273245.4576572493
40.9761501387680.09401389984220.7403559972010.50770289822-0.2314780290791.355257240510.0176741898987-0.08893530778080.123216399483-0.0686724947814-0.03912247077350.1238772880860.007367027168-0.0903366312663-0.0001192461124130.2902931087410.001685260340010.01847664838110.155550001143-0.01464640899750.240480532279-0.8085353680440.9954208602436.8327341106
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 64 )1 - 641 - 64
22chain 'A' and (resid 65 through 125 )65 - 12565 - 125
33chain 'A' and (resid 126 through 155 )126 - 155126 - 155
44chain 'A' and (resid 156 through 294 )156 - 294156 - 294

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