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- PDB-8qfw: Murine pyridoxal phosphatase in complex with 7,8-dihydroxyflavone -

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Basic information

Entry
Database: PDB / ID: 8qfw
TitleMurine pyridoxal phosphatase in complex with 7,8-dihydroxyflavone
ComponentsChronophin
KeywordsHYDROLASE / Phosphatase / Inhibitor / Chronophin
Function / homology
Function and homology information


pyridoxal phosphatase / pyridoxal phosphate catabolic process / actin rod assembly / pyridoxal phosphatase activity / contractile ring / positive regulation of actin filament depolymerization / regulation of modification of postsynaptic structure / dephosphorylation / regulation of mitotic nuclear division / protein-serine/threonine phosphatase ...pyridoxal phosphatase / pyridoxal phosphate catabolic process / actin rod assembly / pyridoxal phosphatase activity / contractile ring / positive regulation of actin filament depolymerization / regulation of modification of postsynaptic structure / dephosphorylation / regulation of mitotic nuclear division / protein-serine/threonine phosphatase / cellular response to ATP / protein serine/threonine phosphatase activity / cleavage furrow / phosphoprotein phosphatase activity / lamellipodium membrane / protein dephosphorylation / heat shock protein binding / regulation of cytokinesis / ruffle membrane / cell-cell junction / actin cytoskeleton / midbody / postsynapse / glutamatergic synapse / magnesium ion binding / protein homodimerization activity / 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
CITRIC ACID / TRIETHYLENE GLYCOL / PHOSPHATE ION / : / Chronophin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchindelin, H. / Gohla, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB688-A11 Germany
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.
History
DepositionSep 5, 2023Deposition 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chronophin
B: Chronophin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,25711
Polymers63,2382
Non-polymers1,0199
Water5,693316
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-32 kcal/mol
Surface area24630 Å2
Unit cell
Length a, b, c (Å)167.011, 167.011, 167.011
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 2 or resid 4...
d_2ens_1(chain "B" and (resid 1 through 2 or resid 4...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETALAALAAA1 - 22 - 3
d_12CYSCYSALAALAAA4 - 195 - 20
d_13GLYGLYLEULEUAA21 - 4422 - 45
d_14ARGARGALAALAAA46 - 7347 - 74
d_15LEULEULEULEUAA75 - 9076 - 91
d_16ALAALAALAALAAA92 - 9393 - 94
d_17LEULEULEULEUAA95 - 9696 - 97
d_18LEULEUSERSERAA100 - 101101 - 102
d_19SERSERTHRTHRAA107 - 156108 - 157
d_110ALAALAGLYGLYAA158 - 190159 - 191
d_111LEULEUARGARGAA192 - 202193 - 203
d_112ALAALATYRTYRAA204 - 213205 - 214
d_113PHEPHEGLNGLNAA215 - 216216 - 217
d_114ILEILETHRTHRAA218 - 219219 - 220
d_115ASPASPTHRTHRAA221 - 229222 - 230
d_116METMETALAALAAA231 - 263232 - 264
d_117ALAALALEULEUAA265 - 267266 - 268
d_118ALAALAGLYGLYAA269 - 270270 - 271
d_119ARGARGASPASPAA272 - 273273 - 274
d_120VALVALGLUGLUAA275 - 291276 - 292
d_121MGMGMGMGAC301
d_122PO4PO4PO4PO4AD302
d_21METMETALAALABB1 - 22 - 3
d_22CYSCYSALAALABB4 - 195 - 20
d_23GLYGLYLEULEUBB21 - 4422 - 45
d_24ARGARGALAALABB46 - 7347 - 74
d_25LEULEULEULEUBB75 - 9076 - 91
d_26ALAALAALAALABB92 - 9393 - 94
d_27LEULEULEULEUBB95 - 9696 - 97
d_28LEULEUTHRTHRBB100 - 156101 - 157
d_29ALAALAGLYGLYBB158 - 190159 - 191
d_210LEULEUARGARGBB192 - 202193 - 203
d_211ALAALATYRTYRBB204 - 213205 - 214
d_212PHEPHEGLNGLNBB215 - 216216 - 217
d_213ILEILETHRTHRBB218 - 219219 - 220
d_214ASPASPTHRTHRBB221 - 229222 - 230
d_215METMETALAALABB231 - 263232 - 264
d_216ALAALALEULEUBB265 - 267266 - 268
d_217ALAALAGLYGLYBB269 - 270270 - 271
d_218ARGARGASPASPBB272 - 273273 - 274
d_219VALVALGLUGLUBB275 - 291276 - 292
d_220MGMGMGMGBI301
d_221PO4PO4PO4PO4BJ302

NCS oper: (Code: givenMatrix: (-0.238859664484, 0.271820396322, 0.932233732937), (-0.152294024333, -0.958628458721, 0.240495339418), (0.959037325048, -0.0845289907249, 0.270374294067)Vector: -19. ...NCS oper: (Code: given
Matrix: (-0.238859664484, 0.271820396322, 0.932233732937), (-0.152294024333, -0.958628458721, 0.240495339418), (0.959037325048, -0.0845289907249, 0.270374294067)
Vector: -19.8303266303, -30.3763939665, 33.5164106966)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Chronophin / Pyridoxal 5'-phosphate phosphatase / Pyridoxal phosphate phosphatase / PLP phosphatase


Mass: 31618.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdxp, Cin, Plp, Plpp / Production host: Escherichia coli (E. coli)
References: UniProt: P60487, protein-serine/threonine phosphatase, pyridoxal phosphatase

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Non-polymers , 7 types, 325 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: Protein solution: 10 mg/ml protein in 50 mM triethanolamine, 250 mM NaCl and 5 mM MgCl2 at pH 7.4 with 3-fold molar excess of 7,8-DHF Reservoir solution 0.1 M phosphate-citrate buffer and 40% v/v PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 52033 / % possible obs: 99.8 % / Redundancy: 41 % / Biso Wilson estimate: 39.35 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.03 / Rrim(I) all: 0.192 / Net I/σ(I): 20.66
Reflection shellResolution: 2→2.12 Å / Redundancy: 40.66 % / Rmerge(I) obs: 3.667 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 8286 / CC1/2: 0.516 / Rpim(I) all: 0.772 / Rrim(I) all: 3.713 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.64 Å / SU ML: 0.253 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1655
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2094 2545 4.89 %
Rwork0.1844 49450 -
obs0.1856 51995 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.19 Å2
Refinement stepCycle: LAST / Resolution: 2→44.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4379 0 66 316 4761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214693
X-RAY DIFFRACTIONf_angle_d0.53076383
X-RAY DIFFRACTIONf_chiral_restr0.0387706
X-RAY DIFFRACTIONf_plane_restr0.0078879
X-RAY DIFFRACTIONf_dihedral_angle_d14.15961807
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.814185696174 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.35091420.34382714X-RAY DIFFRACTION98.41
2.04-2.080.32711310.3012732X-RAY DIFFRACTION99.97
2.08-2.130.3361390.26292731X-RAY DIFFRACTION99.97
2.13-2.180.24721250.24662730X-RAY DIFFRACTION100
2.18-2.230.2561620.22742716X-RAY DIFFRACTION100
2.23-2.290.23921390.22332710X-RAY DIFFRACTION100
2.29-2.360.21971430.21392732X-RAY DIFFRACTION100
2.36-2.440.24751340.20952745X-RAY DIFFRACTION100
2.44-2.520.24661640.21832717X-RAY DIFFRACTION100
2.52-2.620.23811350.19392733X-RAY DIFFRACTION99.93
2.62-2.740.19851130.19892777X-RAY DIFFRACTION100
2.74-2.890.23771430.19242760X-RAY DIFFRACTION99.97
2.89-3.070.22481520.18762726X-RAY DIFFRACTION100
3.07-3.30.24711310.18972762X-RAY DIFFRACTION100
3.31-3.640.18281220.1632777X-RAY DIFFRACTION100
3.64-4.160.18371550.15252751X-RAY DIFFRACTION99.9
4.16-5.240.13411500.13992782X-RAY DIFFRACTION100
5.24-44.640.20841650.18472855X-RAY DIFFRACTION99.8
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)
12.910699679150.5992618772291.241700009783.783335383290.2069267870173.16185621299-0.175010311996-0.426957491705-0.2719516465310.615038624488-0.0119131790298-0.3150724098050.427050729340.4570865330440.2027948014990.4271209603810.068699267460.0402743543150.4353837146090.1023720014390.336350713853-43.9670571938-35.7315716883-10.4327248106
22.383570391710.3789407780040.400895948251.08787067145-0.1131362761373.14369492992-0.1792582306790.02826694266020.420494127850.181996152345-0.01881057137670.0795947276257-0.2419117795680.07221579337390.1990427134240.290262811861-0.04606066971360.01181240286060.2434682266860.03031991184810.438899487962-53.7624742365-23.2969442253-24.5567333377
34.528117642020.4665543957810.532898338427.033464480820.7061493634222.42045205226-0.1916657111650.8952748229430.570899504265-0.675462049873-0.0453554173551-0.0867873979597-0.5352447880310.2683092059620.1297577755980.308629869634-0.0670892720258-0.02265803975260.4288791547630.1042743356490.365719763328-62.6228945876-27.0982587087-45.1650750448
43.749941367961.963676194472.160302727821.593519380320.9083541751042.75417895906-0.03652938024930.1637629594150.0846040514303-0.0132746252149-0.0417829562468-0.03531843571590.0217343801760.1348375863190.04470435229150.295276218309-0.01819903400320.0777665061850.2884305835330.01378245881190.387020275016-61.4148560498-37.2399612795-36.1870183903
53.05408122446-0.4898126824470.3325305102182.517237074660.1711919480083.93504979757-0.122858029933-0.272202085787-0.1520356883250.372572013852-0.0824254092340.2310345115430.6058020200180.03972036764120.1488684458020.411134832746-0.01843146713660.08771202842790.2938297048030.06347540679890.317889420841-50.5996387618-38.3301742406-15.5331503925
60.7123531382470.03647073847171.026283613910.9360662658431.092843611272.815436185880.222896615939-0.9936733178510.3466623292621.771116685130.183716983948-0.339170258051-0.08628615611530.356383457896-0.1733305394231.0403843846-0.154545299648-0.2956468820530.888495015683-0.07079245775740.474297757616-28.07794005787.69740961364-8.75182982582
74.222578696610.4263440125890.5284752306872.2277670323-0.1000541858961.849069130990.204108366442-0.130546780976-0.5968013066690.289753052927-0.0302016319453-0.2219191909470.2788328653510.198185471602-0.2244893465430.493399950763-0.0556659221247-0.07687338067970.3246019843510.07491366357890.406251767735-35.998552607-5.59324658788-22.9282666122
81.112983569730.022714710531-0.3638971558844.48467949358-0.9215849613282.287264114270.102835099275-0.0213412507771-0.285594803636-0.1629604944030.0690462997260.5197768119980.370782761154-0.275025571202-0.05129614693260.349656061215-0.112434829682-0.1027671300340.2709981421230.07784446786930.40099198792-53.0689156851-5.28726030988-37.0440198738
91.96562510896-0.2502504907621.015234319443.01105100465-1.760418114373.300572964640.117335064091-0.218408488262-0.08669569901780.1145890398430.1514286976860.3424353176080.0879371416675-0.164109332872-0.2291018722810.334468621947-0.0714982504165-0.004087106993520.2267527182430.0534593122650.286989036992-49.05849491745.9143814566-32.3949350543
104.297969318650.413651041335-0.9099738189452.841243783870.07385527447694.028090375640.289717018916-0.6707579263990.2441952998040.748116877905-0.0936759892599-0.325032989793-0.2612215112590.44101769364-0.1384580885450.616883740291-0.153144857309-0.0756970969290.449852753782-0.04205853302720.275740129275-32.551298652110.2749535495-15.8696592619
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 25 )AA0 - 251 - 26
22chain 'A' and (resid 26 through 100 )AA26 - 10027 - 101
33chain 'A' and (resid 101 through 151 )AA101 - 151102 - 152
44chain 'A' and (resid 152 through 221 )AA152 - 221153 - 222
55chain 'A' and (resid 222 through 291 )AA222 - 291223 - 292
66chain 'B' and (resid 1 through 25 )BH1 - 251 - 25
77chain 'B' and (resid 26 through 100)BH26 - 10026 - 100
88chain 'B' and (resid 101 through 151)BH101 - 151101 - 146
99chain 'B' and (resid 152 through 221 )BH152 - 221147 - 216
1010chain 'B' and (resid 222 through 291 )BH222 - 291217 - 286

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