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- PDB-3b1r: Structure of Burkholderia thailandensis nucleoside kinase (BthNK)... -

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Basic information

Entry
Database: PDB / ID: 3b1r
TitleStructure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with AMP-Mg-AMP
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
ADENOSINE MONOPHOSPHATE / Ribokinase, putative
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
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_ref_seq_dif / struct_site
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_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_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)214,73725
Polymers210,4006
Non-polymers4,33719
Water18,3931021
1
A: Ribokinase, putative
D: Ribokinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5959
Polymers70,1332
Non-polymers1,4627
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-68 kcal/mol
Surface area22690 Å2
MethodPISA
2
B: Ribokinase, putative
E: Ribokinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5718
Polymers70,1332
Non-polymers1,4376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-65 kcal/mol
Surface area22430 Å2
MethodPISA
3
C: Ribokinase, putative
F: Ribokinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5718
Polymers70,1332
Non-polymers1,4376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-65 kcal/mol
Surface area22450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.222, 125.222, 115.002
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Ribokinase, putative / Nucleoside kinase


Mass: 35066.723 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
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1021 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.1M Tris, 0.2M MgCl2, 20% PEG 8000, pH 8.5, 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: Mar 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.501
11-H, H+K, -L20.499
ReflectionResolution: 2→50 Å / Num. obs: 136213 / % possible obs: 99 % / Redundancy: 5.6 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 4.3 / % 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→42.35 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.659 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The refinement was performed using twinning operator (-H, H+K, -L) and with estimating the twinning fraction.
RfactorNum. reflection% reflectionSelection details
Rfree0.20398 7058 5.2 %RANDOM
Rwork0.16728 ---
obs0.16916 129118 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.941 Å2
Baniso -1Baniso -2Baniso -3
1-6.31 Å20 Å20 Å2
2--6.31 Å20 Å2
3----12.62 Å2
Refinement stepCycle: LAST / Resolution: 2→42.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14232 0 283 1021 15536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02114875
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.97620226
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05351868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23123.314691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.543152311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.97615126
X-RAY DIFFRACTIONr_chiral_restr0.0880.22216
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111468
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_it0.5011.59201
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.902214677
X-RAY DIFFRACTIONr_scbond_it1.41735674
X-RAY DIFFRACTIONr_scangle_it2.1674.55542
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 504 -
Rwork0.164 9444 -
obs--98.3 %

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