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- PDB-6yjz: Crystal structure of mouse pyridoxal kinase in apo form -

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Basic information

Entry
Database: PDB / ID: 6yjz
TitleCrystal structure of mouse pyridoxal kinase in apo form
ComponentsPyridoxal Kinase
KeywordsTRANSFERASE / PDXK / PLP / PL / Vitamin B6 / Enzyme
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKasaragod, V.B. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHI425/8-2 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Pyridoxal kinase inhibition by artemisinins down-regulates inhibitory neurotransmission.
Authors: Kasaragod, V.B. / Pacios-Michelena, A. / Schaefer, N. / Zheng, F. / Bader, N. / Alzheimer, C. / Villmann, C. / Schindelin, H.
History
DepositionApr 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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

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Assembly

Deposited unit
A: Pyridoxal Kinase
B: Pyridoxal Kinase
C: Pyridoxal Kinase
D: Pyridoxal Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,62926
Polymers140,8494
Non-polymers1,78022
Water3,369187
1
A: Pyridoxal Kinase
B: Pyridoxal Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,58615
Polymers70,4252
Non-polymers1,16113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint16 kcal/mol
Surface area25040 Å2
MethodPISA
2
C: Pyridoxal Kinase
D: Pyridoxal Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,04311
Polymers70,4252
Non-polymers6199
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint7 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)279.135, 53.433, 109.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Pyridoxal Kinase


Mass: 35212.355 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
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: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.18-0.24 M sodium thiocyanate and 18-26% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.45→47.32 Å / Num. obs: 57180 / % possible obs: 95.6 % / Redundancy: 3.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.093 / Rrim(I) all: 0.08752 / Net I/σ(I): 9.1
Reflection shellResolution: 2.45→2.53 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5965 / CC1/2: 0.572 / Rpim(I) all: 0.7 / Rrim(I) all: 0.6776 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XYT

2xyt


Resolution: 2.45→47.32 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27
RfactorNum. reflection% reflection
Rfree0.26 2930 5.12 %
Rwork0.216 --
obs0.2183 57174 95.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→47.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9400 0 116 187 9703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029671
X-RAY DIFFRACTIONf_angle_d0.52513062
X-RAY DIFFRACTIONf_dihedral_angle_d19.0973594
X-RAY DIFFRACTIONf_chiral_restr0.0421496
X-RAY DIFFRACTIONf_plane_restr0.0031691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.490.32881360.30362690X-RAY DIFFRACTION100
2.49-2.530.31941390.30282688X-RAY DIFFRACTION100
2.53-2.580.35981370.2922662X-RAY DIFFRACTION100
2.58-2.630.33211320.27492703X-RAY DIFFRACTION99
2.63-2.680.29111280.2722707X-RAY DIFFRACTION99
2.68-2.740.33421640.26942647X-RAY DIFFRACTION99
2.74-2.80.29051650.25792625X-RAY DIFFRACTION99
2.8-2.870.29871640.25352587X-RAY DIFFRACTION98
2.87-2.950.30851200.25692703X-RAY DIFFRACTION98
2.95-3.040.31841510.262615X-RAY DIFFRACTION97
3.04-3.140.28161520.25442589X-RAY DIFFRACTION96
3.14-3.250.3011610.2412515X-RAY DIFFRACTION96
3.25-3.380.29611430.22882553X-RAY DIFFRACTION94
3.38-3.530.23111110.23292545X-RAY DIFFRACTION92
3.53-3.720.26151180.21522441X-RAY DIFFRACTION91
3.72-3.950.24781380.192511X-RAY DIFFRACTION92
3.95-4.260.20021450.18392472X-RAY DIFFRACTION91
4.26-4.680.20551100.15732485X-RAY DIFFRACTION90
4.69-5.360.20741320.17632484X-RAY DIFFRACTION90
5.36-6.750.28051320.21182495X-RAY DIFFRACTION90
6.75-47.320.23711520.18982527X-RAY DIFFRACTION89

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