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- PDB-3b1o: Structure of Burkholderia thailandensis nucleoside kinase (BthNK)... -

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Basic information

Entry
Database: PDB / ID: 3b1o
TitleStructure of Burkholderia thailandensis nucleoside kinase (BthNK) in ligand-free form
ComponentsRibokinase, putative
KeywordsTRANSFERASE / Rossmann Fold / kinase / ATP binding / Mg binding / Nucleoside binding
Function / homology
Function and homology information


kinase activity / nucleotide binding
Similarity search - Function
pfkB family of carbohydrate kinases signature 1. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribokinase, putative
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYasutake, Y. / Ota, H. / Hino, E. / Sakasegawa, S. / Tamura, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structures of Burkholderia thailandensis nucleoside kinase: implications for the catalytic mechanism and nucleoside selectivity
Authors: Yasutake, Y. / Ota, H. / Hino, E. / Sakasegawa, S. / Tamura, T.
History
DepositionJul 5, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribokinase, putative
B: Ribokinase, putative


Theoretical massNumber of molelcules
Total (without water)71,5032
Polymers71,5032
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-22 kcal/mol
Surface area25160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.359, 85.359, 160.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ribokinase, putative / Nucleoside kinase


Mass: 35751.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: Bth_I1158 / Plasmid: pTip-QC2 / Production host: Rhodococcus erythropolis (bacteria) / Strain (production host): L88 / References: UniProt: Q2SZE4, EC: 2.7.1.143
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.05 Å3/Da / Density % sol: 39.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.3
Details: 0.1M CHES, 0.2M NaCl, 1.4M ammonium sulfate, pH 9.3, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 22, 2010
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 35578 / Num. obs: 35578 / % possible obs: 100 % / Redundancy: 12 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 8.3 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B1N

3b1n


Resolution: 2.1→42.68 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.886 / SU B: 13.86 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27663 1669 4.9 %RANDOM
Rwork0.23574 ---
obs0.23779 32351 95.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.876 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4706 0 0 194 4900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214803
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.9536510
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.695614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37823.392227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1815763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3111541
X-RAY DIFFRACTIONr_chiral_restr0.080.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213728
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.291.53039
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.51524843
X-RAY DIFFRACTIONr_scbond_it0.9731764
X-RAY DIFFRACTIONr_scangle_it1.4814.51667
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 132 -
Rwork0.285 2193 -
obs--90.26 %
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)
10.5177-0.38430.50021.9881-3.65687.3137-0.0575-0.03450.1030.17810.30070.1661-0.6828-0.6579-0.24330.30280.0674-0.04930.19570.00760.1965-20.725438.4253-26.8175
22.22480.4820.04211.46240.4031.3629-0.0010.0032-0.1632-0.06850.0103-0.0236-0.0459-0.0022-0.00930.06250.026-0.00270.15020.01290.1259-15.426219.9326-17.7859
34.60160.55050.11943.12480.97963.42950.0339-0.1029-0.09760.0443-0.07020.3079-0.1008-0.25040.03630.00870.0325-0.00210.225-0.00610.1315-34.06620.1554-14.2449
40.6157-1.97090.57667.62260.4464.8494-0.1123-0.03450.16550.01440.1737-0.7571-0.41040.1357-0.06140.39-0.01830.01480.22030.02680.2625-13.058239.5139-29.3384
50.4182-0.29330.23210.9492-0.74650.7538-0.0218-0.20530.0420.5567-0.0321-0.2138-0.40130.18890.05390.653-0.0977-0.05030.3167-0.05410.3206-7.864263.7736-21.4104
63.57110.1237-0.49257.2491-0.31461.0420.12670.33690.3807-0.4149-0.1269-0.3677-0.10940.26520.00020.5811-0.19410.01360.5992-0.03550.37786.451965.9527-32.8682
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 45
2X-RAY DIFFRACTION2A46 - 221
3X-RAY DIFFRACTION3A222 - 314
4X-RAY DIFFRACTION4B2 - 45
5X-RAY DIFFRACTION5B46 - 219
6X-RAY DIFFRACTION6B220 - 304

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