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- PDB-3ibq: Crystal structure of pyridoxal kinase from Lactobacillus plantaru... -

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Basic information

Entry
Database: PDB / ID: 3ibq
TitleCrystal structure of pyridoxal kinase from Lactobacillus plantarum in complex with ATP
ComponentsPyridoxal kinase
KeywordsTRANSFERASE / Pyridoxal kinase / ATP / PSI-II / 11208c / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / Kinase
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 / pyridoxal kinase / :
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBagaria, A. / Kumaran, D. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of pyridoxal kinase from Lactobacillus plantarum in complex with ATP
Authors: Bagaria, A. / Kumaran, D. / Burley, S.K. / Swaminathan, S.
History
DepositionJul 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9443
Polymers30,4131
Non-polymers5312
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Pyridoxal kinase
hetero molecules

A: Pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8886
Polymers60,8252
Non-polymers1,0634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4930 Å2
ΔGint-53 kcal/mol
Surface area21340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.357, 69.576, 132.369
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


Mass: 30412.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: WCFS1 / Gene: pdx, lp_0863 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli)
References: UniProt: Q88YB5, UniProt: F9UM74*PLUS, pyridoxal kinase
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M MgCl2, 0.1M HEPES pH 6.5, 25% PEG3350, 20mM ATP , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2009 / Details: Mirrors
RadiationMonochromator: Si(111)channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→38.46 Å / Num. all: 20473 / Num. obs: 19397 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 6.6 / Num. unique all: 1406 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H74

3h74


Resolution: 2→38.46 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.47 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.165 / ESU R Free: 0.152 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21946 1056 5.2 %RANDOM
Rwork0.17531 ---
obs0.17759 19397 100 %-
all-20473 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.029 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→38.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 32 169 2238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222108
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.9822898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0495271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11825.23386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09415313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.106159
X-RAY DIFFRACTIONr_chiral_restr0.1170.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021581
X-RAY DIFFRACTIONr_nbd_refined0.2130.2947
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21450
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2950.2133
X-RAY DIFFRACTIONr_metal_ion_refined0.1930.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5170.224
X-RAY DIFFRACTIONr_mcbond_it1.1921.51391
X-RAY DIFFRACTIONr_mcangle_it1.64122161
X-RAY DIFFRACTIONr_scbond_it2.6713831
X-RAY DIFFRACTIONr_scangle_it4.0324.5737
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 95 -
Rwork0.184 1406 -
obs--100 %

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