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- PDB-4ek2: The structure of nucleoside diphosphate kinase (NDK) from Burkhol... -

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Basic information

Entry
Database: PDB / ID: 4ek2
TitleThe structure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis bound to deoxyadenosine monophosphate
ComponentsNucleoside diphosphate kinaseNucleoside-diphosphate kinase
KeywordsTRANSFERASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / dAMP / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionApr 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 13, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0May 29, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4958
Polymers31,8742
Non-polymers6206
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-28 kcal/mol
Surface area13110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.680, 90.680, 90.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-389-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nucleoside diphosphate kinase / Nucleoside-diphosphate kinase / NDK / NDP kinase / Nucleoside-2-P kinase


Mass: 15937.228 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: ndk, BTH_I2231 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2SWE7, nucleoside-diphosphate kinase

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Non-polymers , 5 types, 281 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Deoxyadenosine monophosphate


Mass: 331.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6P
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: ButhA.00438.a.A1 PS01186 at 42.64 mg/mL in 1.5 M ammonium sulfate, 0.1 M Bis-Tris propane, pH 7.0, 10 mM dAMP, cryoprotectant: 15% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40.553 Å / Num. obs: 25415 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.831 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 30.21
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.050.2197.95811593184.4
2.05-2.110.1910.4215941709191.9
2.11-2.170.19512.1751031772199.7
2.17-2.240.21212.8651871668195.5
2.24-2.310.11324.6634321543190.2
2.31-2.390.14216.855041641199.9
2.39-2.480.12718.74495215701100
2.48-2.580.11319.79472815511100
2.58-2.70.10122.18396014651100
2.7-2.830.08326.21354014221100
2.83-2.980.06731.63287213441100
2.98-3.160.05536.7214712761100
3.16-3.380.04344.41157112181100
3.38-3.650.03852.4447311251100
3.65-40.03859.73761033198
4-4.470.02571.17881946199.9
4.47-5.160.02769.079248521100
5.16-6.320.03651.58237431100
6.32-8.940.02763.961245851100
8.94-40.5530.01891.092723359196.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DUT

4dut


Resolution: 2→40.553 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.1901 / WRfactor Rwork: 0.1595 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8646 / SU B: 6.791 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1652 / SU Rfree: 0.1516 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 1295 5.1 %RANDOM
Rwork0.1897 ---
obs0.1916 25383 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.97 Å2 / Biso mean: 16.6122 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2→40.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 36 275 2473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222285
X-RAY DIFFRACTIONr_bond_other_d0.0010.021546
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.9713099
X-RAY DIFFRACTIONr_angle_other_deg0.92333756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7295294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72223.611108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02215375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6411519
X-RAY DIFFRACTIONr_chiral_restr0.0840.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212584
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02484
X-RAY DIFFRACTIONr_mcbond_it0.6151.51431
X-RAY DIFFRACTIONr_mcbond_other0.1591.5571
X-RAY DIFFRACTIONr_mcangle_it1.10322293
X-RAY DIFFRACTIONr_scbond_it1.8853854
X-RAY DIFFRACTIONr_scangle_it3.1494.5799
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 86 -
Rwork0.19 1504 -
all-1590 -
obs--84.39 %
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)
11.6470.16890.07860.6818-0.26780.6444-0.03670.1394-0.1117-0.06460.03980.0290.0174-0.0495-0.00310.0318-0.00120.010.0415-0.02320.0299-16.214824.2287-5.2175
25.62790.53621.23343.2572-0.49762.9684-0.01920.4131-0.8634-0.4572-0.0452-0.24450.40230.13920.06440.16760.00110.06480.0307-0.08030.2802-11.56397.2396-1.3805
33.55710.06980.87011.00860.00981.93520.03320.319-0.2364-0.18610.0323-0.00390.1496-0.095-0.06540.0679-0.00410.00910.0696-0.03310.0375-18.39921.2666-11.1139
41.86920.4498-0.12621.07480.12220.9838-0.0430.2931-0.261-0.03510.0712-0.10830.0928-0.0434-0.02820.03420.00280.00020.0623-0.04060.0393-17.479618.6421-7.4939
51.06270.0199-0.16970.6971-0.00820.94780.02-0.01180.04110.03950.02840.0359-0.082-0.0277-0.04850.040.00530.01030.0212-0.00250.0358-16.456336.47483.384
61.58880.42691.73947.59861.85865.43980.2047-0.22930.1411-0.0817-0.11070.2349-0.5989-0.2252-0.0940.24490.02130.09490.0908-0.0150.0393-26.923247.702212.6425
73.0983-0.56320.31451.4745-0.13610.32740.0586-0.10220.07240.08050.0142-0.1152-0.11020.0036-0.07280.0690.00130.02310.0298-0.01010.0311-11.472441.01196.0962
80.7919-0.0441-0.23571.4335-0.2721.35960.0829-0.02290.12140.0626-0.01610.0443-0.1788-0.0079-0.06680.0334-0.00510.02750.0195-0.01340.0536-14.864140.8527.1162
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 45
2X-RAY DIFFRACTION2A46 - 70
3X-RAY DIFFRACTION3A71 - 94
4X-RAY DIFFRACTION4A95 - 141
5X-RAY DIFFRACTION5B2 - 48
6X-RAY DIFFRACTION6B49 - 67
7X-RAY DIFFRACTION7B68 - 93
8X-RAY DIFFRACTION8B94 - 141

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