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

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Basic information

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


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / 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
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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
DepositionFeb 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 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

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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)32,2947
Polymers31,8742
Non-polymers4205
Water1,02757
1
A: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0693
Polymers15,9371
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2254
Polymers15,9371
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.720, 80.720, 112.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

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Components

#1: Protein 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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: ButhA.00438.a.A1 PS01186 at 42.64 mg/mL, 1.5 M ammonium sulfate, 0.1 M Bis-Tris propane, pH 7.0, 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: Jan 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→38.007 Å / Num. all: 13496 / Num. obs: 13496 / % possible obs: 99.6 % / Rmerge(I) obs: 0.097 / Rsym value: 0.067 / Net I/σ(I): 25.98
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.5-2.570.5254.13684996899.8
2.57-2.640.4085.15678795899.6
2.64-2.710.3266.26651591499.7
2.71-2.80.2767.05645990499.9
2.8-2.890.2248.39621787899.8
2.89-2.990.16911597683799.6
2.99-3.10.13713.09589982399.8
3.1-3.230.10217.2565679899.8
3.23-3.370.07822.17535775099.7
3.37-3.540.06328.97518473099.7
3.54-3.730.05634.1485668899.3
3.73-3.950.04341.42463566299.1
3.95-4.230.03350.53439762799.2
4.23-4.560.03158.39390357499.5
4.56-50.02856.12379054499.6
5-5.590.03545.64342649999.8
5.59-6.460.03348.793006447100
6.46-7.910.02456.272579388100
7.91-11.180.01676.281955313100
11.180.01671.8697319293.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.64 Å
Translation3.5 Å19.64 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PJ9

3pj9


Resolution: 2.5→38.007 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.2205 / WRfactor Rwork: 0.1782 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8038 / SU B: 16.448 / SU ML: 0.186 / SU R Cruickshank DPI: 0.3695 / SU Rfree: 0.2713 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.37 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2635 675 5 %RANDOM
Rwork0.2111 ---
obs0.2138 13447 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.63 Å2 / Biso mean: 37.2923 Å2 / Biso min: 11.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 21 57 2088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192059
X-RAY DIFFRACTIONr_bond_other_d0.0030.021336
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9642794
X-RAY DIFFRACTIONr_angle_other_deg0.94733249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9623.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81815314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0661515
X-RAY DIFFRACTIONr_chiral_restr0.0780.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212346
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02421
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 46 -
Rwork0.288 800 -
all-846 -
obs--99.65 %
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)
12.4788-0.0912-0.34762.4519-0.29122.87390.06450.0758-0.171-0.13580.0214-0.11710.16750.1423-0.08590.08620.0298-0.02040.063-0.02040.037420.16069.2029-2.587
212.6237-1.9076-0.18264.5071-1.7950.8503-0.32090.554-1.3064-0.5176-0.0743-0.41960.38550.01680.39520.48810.21450.23880.3918-0.15030.391331.87145.9355-14.2515
32.74950.34020.96492.2067-0.26163.69870.1256-0.1252-0.35430.1394-0.0812-0.08430.3107-0.0367-0.04440.13020.01920.00970.0595-0.00620.106621.44412.89411.8124
42.44841.28690.72064.2571.00522.60010.04650.1005-0.2486-0.1097-0.0816-0.16120.28980.08750.03510.09640.0487-0.01260.0694-0.00670.054123.57694.9994-1.7469
52.8881-0.3654-0.47873.4802-0.3791.79930.13260.20640.0858-0.11410.00720.2554-0.1892-0.2017-0.13980.0820.0571-0.01370.11050.07580.11442.0375-6.035921.8433
62.0121.0715-5.36391.28521.117537.1836-0.03420.00190.4563-0.1646-0.21140.4611-0.3029-0.60080.24560.55670.26530.11010.40350.08520.379810.6265-13.81498.979
76.2068-11.08272.977230.56364.6310.61641.00910.0593-0.7102-2.1895-0.29860.88430.2179-0.073-0.71050.6209-0.01280.04560.23810.09310.278911.8823-5.31249.62
81.8857-1.2150.06182.7419-1.2251.38320.13810.1422-0.0221-0.11090.15940.449-0.0968-0.3517-0.29750.06270.049-0.03850.18980.09320.1666-1.7508-9.792118.0571
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 50
2X-RAY DIFFRACTION2A51 - 69
3X-RAY DIFFRACTION3A70 - 93
4X-RAY DIFFRACTION4A94 - 141
5X-RAY DIFFRACTION5B3 - 45
6X-RAY DIFFRACTION6B46 - 63
7X-RAY DIFFRACTION7B64 - 69
8X-RAY DIFFRACTION8B70 - 141

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