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- PDB-3b1q: Structure of Burkholderia thailandensis nucleoside kinase (BthNK)... -

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Basic information

Entry
Database: PDB / ID: 3b1q
TitleStructure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with inosine
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
ACETATE ION / INOSINE / Ribokinase, putative
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _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: Ribokinase, putative
B: Ribokinase, putative
C: Ribokinase, putative
D: Ribokinase, putative
E: Ribokinase, putative
F: Ribokinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,36649
Polymers214,5096
Non-polymers4,85743
Water18,8981049
1
A: Ribokinase, putative
F: Ribokinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,83516
Polymers71,5032
Non-polymers1,33214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-71 kcal/mol
Surface area23980 Å2
MethodPISA
2
B: Ribokinase, putative
D: Ribokinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,90212
Polymers71,5032
Non-polymers1,39910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-57 kcal/mol
Surface area24860 Å2
MethodPISA
3
C: Ribokinase, putative
E: Ribokinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,62921
Polymers71,5032
Non-polymers2,12619
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-90 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.110, 85.897, 86.872
Angle α, β, γ (deg.)66.33, 68.47, 67.81
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Ribokinase, putative / Nucleoside kinase


Mass: 35751.480 Da / Num. of mol.: 6
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

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Non-polymers , 5 types, 1092 molecules

#2: Chemical
ChemComp-NOS / INOSINE


Mass: 268.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H12N4O5
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1049 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4
Details: 0.1M Na acetate, 0.2M Ca acetate, 26% PEG 400, pH 4.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 21, 2009
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: 1.7→50 Å / Num. obs: 208756 / % possible obs: 97.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 19.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.8 / % possible all: 94

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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: 1.7→47.78 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.774 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20667 10501 5 %RANDOM
Rwork0.17578 ---
obs0.17733 198251 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.609 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20.96 Å20.16 Å2
2---0.57 Å20.3 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13886 0 314 1049 15249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02114533
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.841.97119646
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08751835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24823.199669
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69152270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.09215126
X-RAY DIFFRACTIONr_chiral_restr0.1330.22136
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02111183
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_it1.071.59056
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8214374
X-RAY DIFFRACTIONr_scbond_it2.91235477
X-RAY DIFFRACTIONr_scangle_it4.4964.55259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.704→1.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 727 -
Rwork0.261 13694 -
obs--100 %
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)
11.9242-0.30130.10151.0069-0.6041.09640.0335-0.0276-0.2214-0.042-0.0133-0.01790.09680.0385-0.02020.01170.0065-0.00130.00670.00880.038930.018222.593973.8551
21.4232-0.0386-0.89631.41470.01141.3028-0.01820.10560.0898-0.15550.03620.00070.0641-0.0204-0.0180.08180.0089-0.00430.03370.01460.010336.941243.99827.4592
31.0095-0.46790.36462.24790.28311.26210.0067-0.10480.04650.0411-0.04640.0594-0.0354-0.05160.03970.020.0040.00490.0229-0.00360.008958.113842.3729-13.9499
40.5448-0.45140.25782.0675-0.14351.1219-0.01740.07920.0527-0.2110.00860.03150.00110.04190.00880.0872-0.0133-0.03620.05740.0080.0415-4.802854.678729.2882
51.58140.2398-0.03210.4857-0.59891.3160.0171-0.02410.03980.07460.01970.1295-0.1032-0.1651-0.03680.01350.0080.01990.0392-0.02410.067144.07845.4758-4.3
61.0639-0.2924-0.93981.33320.52731.1186-0.0296-0.0182-0.15950.0833-0.02390.01460.05950.00580.05360.04470.0144-0.01110.0652-0.03290.105819.883310.599533.8854
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 311
2X-RAY DIFFRACTION2B2 - 313
3X-RAY DIFFRACTION3C2 - 313
4X-RAY DIFFRACTION4D2 - 316
5X-RAY DIFFRACTION5E2 - 313
6X-RAY DIFFRACTION6F2 - 311

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