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- PDB-3zs7: Crystal structure of pyridoxal kinase from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 3zs7
TitleCrystal structure of pyridoxal kinase from Trypanosoma brucei
ComponentsPYRIDOXAL KINASE
KeywordsTRANSFERASE / SLEEPING SICKNESS
Function / homology
Function and homology information


pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / ATP binding / cytosol
Similarity search - Function
Pyridoxine kinase / Pyridoxamine kinase/Phosphomethylpyrimidine kinase / Phosphomethylpyrimidine kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / pyridoxal kinase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAlphey, M.S. / Jones, D.C. / Fairlamb, A.H.
CitationJournal: Mol.Microbiol. / Year: 2012
Title: Chemical, Genetic and Structural Assessment of Pyridoxal Kinase as a Drug Target in the African Trypanosome.
Authors: Jones, D.C. / Alphey, M.S. / Wyllie, S. / Fairlamb, A.H.
History
DepositionJun 23, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYRIDOXAL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9763
Polymers33,3741
Non-polymers6022
Water1,62190
1
A: PYRIDOXAL KINASE
hetero molecules

A: PYRIDOXAL KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9536
Polymers66,7482
Non-polymers1,2044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5100 Å2
ΔGint-31.5 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.210, 80.000, 106.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PYRIDOXAL KINASE / PYRIDOXINE/PYRIDOXAL/PYRIDOXAMINE KINASE


Mass: 33374.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ATP APPEARS IN TWO ALTERNATE CONFORMATIONS / Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Strain: TREU927 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15927, pyridoxal kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.3 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 5, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 18739 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.1 / % possible all: 84.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YXT

2yxt


Resolution: 2→19.71 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.079 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES IN DISORDERED REGIONS (121-129 189-191, AND 265-274) WERE LEFT OUT OF THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.26537 970 5 %RANDOM
Rwork0.2194 ---
obs0.22171 18420 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.564 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å20 Å2
2---0.19 Å20 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 2→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2147 0 36 90 2273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222276
X-RAY DIFFRACTIONr_bond_other_d0.0010.021474
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9893109
X-RAY DIFFRACTIONr_angle_other_deg0.85633590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68123.36798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32915358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0861515
X-RAY DIFFRACTIONr_chiral_restr0.0690.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212479
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02469
X-RAY DIFFRACTIONr_nbd_refined0.2190.2450
X-RAY DIFFRACTIONr_nbd_other0.1770.21428
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21072
X-RAY DIFFRACTIONr_nbtor_other0.0870.21139
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2101
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1830.215
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1810.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7981.51381
X-RAY DIFFRACTIONr_mcbond_other0.1431.5561
X-RAY DIFFRACTIONr_mcangle_it1.44522233
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5613895
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3434.5874
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 68 -
Rwork0.248 1292 -
obs--100 %

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