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- PDB-5zwa: Crystal structure of Pyridoxal kinase (PdxK) from Salmonella typh... -

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Basic information

Entry
Database: PDB / ID: 5zwa
TitleCrystal structure of Pyridoxal kinase (PdxK) from Salmonella typhimurium in complex with ADP, PL-linked to Lys233 via Schiff base in protomer A and the product (PLP) in protomer B
Components(Pyridoxine/pyridoxal/pyridoxamine ...) x 2
KeywordsTRANSFERASE / Pyridoxal kinase / bound phosphate / Salmonella typhimurium
Function / homology
Function and homology information


hydroxymethylpyrimidine kinase activity / pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / phosphorylation / magnesium ion binding / zinc ion binding / ATP binding / cytosol
Similarity search - Function
Pyridoxine/pyridoxal/pyridoxamine kinase / 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'-DIPHOSPHATE / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Pyridoxine/pyridoxal/pyridoxamine kinase / Pyridoxine/pyridoxal/pyridoxamine kinase
Similarity search - Component
Biological speciesSalmonella choleraesuis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsDeka, G. / Benazir, J.F. / Kalyani, J.N. / Savithri, H.S. / Murthy, M.R.N.
Funding support India, 2items
OrganizationGrant numberCountry
BT/ PR7021/BRB/10/1142/2012 India
SR/S2/ JCB-12/2005/9.5.2006 India
CitationJournal: Febs J. / Year: 2019
Title: Structural and functional studies on Salmonella typhimurium pyridoxal kinase: the first structural evidence for the formation of Schiff base with the substrate.
Authors: Deka, G. / Kalyani, J.N. / Jahangir, F.B. / Sabharwal, P. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionMay 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridoxine/pyridoxal/pyridoxamine kinase
B: Pyridoxine/pyridoxal/pyridoxamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,64927
Polymers64,4282
Non-polymers2,22125
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-70 kcal/mol
Surface area20360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.260, 72.260, 244.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 17 - 283 / Label seq-ID: 17 - 283

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Pyridoxine/pyridoxal/pyridoxamine ... , 2 types, 2 molecules AB

#1: Protein Pyridoxine/pyridoxal/pyridoxamine kinase / PN/PL/PM kinase


Mass: 32287.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella choleraesuis (bacteria) / Gene: pdxK / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: A0A0M0PWM4, UniProt: A0A0F7J8S0*PLUS, pyridoxal kinase
#2: Protein Pyridoxine/pyridoxal/pyridoxamine kinase / PN/PL/PM kinase


Mass: 32139.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella choleraesuis (bacteria) / Gene: pdxK / Plasmid: pET-22b(+) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: A0A0M0PWM4, UniProt: A0A0F7J8S0*PLUS, pyridoxal kinase

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Non-polymers , 8 types, 282 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#9: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.5 / Details: 50% PEG 4000, 10% Glycerol, 100 mM Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.45→62.23 Å / Num. obs: 23479 / % possible obs: 94.3 % / Redundancy: 14.9 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.03 / Rrim(I) all: 0.14 / Net I/σ(I): 15.7
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 15.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 3297 / Rpim(I) all: 0.11 / Rrim(I) all: 0.5 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZW9

5zw9


Resolution: 2.45→62.23 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.827 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.527 / ESU R Free: 0.264 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23458 1156 4.9 %RANDOM
Rwork0.21639 ---
obs0.21728 22240 94.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.782 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å2-0 Å2-0 Å2
2--0.58 Å2-0 Å2
3----1.16 Å2
Refinement stepCycle: 1 / Resolution: 2.45→62.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 137 259 4330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.024165
X-RAY DIFFRACTIONr_bond_other_d0.0020.024036
X-RAY DIFFRACTIONr_angle_refined_deg0.9991.9995673
X-RAY DIFFRACTIONr_angle_other_deg0.80339260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.765534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70324.851134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26415631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8351514
X-RAY DIFFRACTIONr_chiral_restr0.0520.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214576
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02839
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6512.6472136
X-RAY DIFFRACTIONr_mcbond_other0.6512.6472135
X-RAY DIFFRACTIONr_mcangle_it1.2043.962667
X-RAY DIFFRACTIONr_mcangle_other1.2043.9612668
X-RAY DIFFRACTIONr_scbond_it0.5182.8132029
X-RAY DIFFRACTIONr_scbond_other0.5182.8132029
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9254.163006
X-RAY DIFFRACTIONr_long_range_B_refined3.70721.6524716
X-RAY DIFFRACTIONr_long_range_B_other3.70721.6524716
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14788 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 81 -
Rwork0.237 1587 -
obs--92.92 %

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