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- PDB-4hr2: Structure of nucleoside diphosphate kinase (NDK) from Burkholderi... -

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Basic information

Entry
Database: PDB / ID: 4hr2
TitleStructure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis bound to ADP
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
ADENOSINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Structure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis bound to ADP
Authors: Clifton, M.C. / Abendroth, J.A.
History
DepositionOct 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,7294
Polymers31,8742
Non-polymers8542
Water5,549308
1
A: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3642
Polymers15,9371
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3642
Polymers15,9371
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-22 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.240, 91.240, 90.190
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-781-

HOH

21B-789-

HOH

31B-841-

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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.94 Å3/Da / Density % sol: 58.23 %
Crystal growTemperature: 298 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, 1mM ADP, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: Sep 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→40.427 Å / Num. obs: 27811 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.593 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.37
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.95-20.4422.765646195795.3
2-2.060.26756671195397.3
2.06-2.120.2276.367278193999.3
2.12-2.180.2176.987811188399.4
2.18-2.250.10415.597280176195
2.25-2.330.14611.836928154586.7
2.33-2.420.1411.578718173299.9
2.42-2.520.12614.329584166899.9
2.52-2.630.11115.4494631603100
2.63-2.760.0918.7790941528100
2.76-2.910.07321.788787147499.9
2.91-3.080.05627.1682041385100
3.08-3.30.04533.777721309100
3.3-3.560.03837.847292123299.8
3.56-3.90.03848.346211111697.8
3.9-4.360.02752.415955101798.3
4.36-5.030.02555.72534492299.6
5.03-6.170.03342.92457780199.8
6.17-8.720.02651.68346462398.3
8.720.01969.07177336390.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.43 Å
Translation2.5 Å40.43 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EK2

4ek2


Resolution: 1.95→40.427 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.892 / WRfactor Rfree: 0.2001 / WRfactor Rwork: 0.1737 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8294 / SU B: 5.772 / SU ML: 0.091 / SU R Cruickshank DPI: 0.1636 / SU Rfree: 0.1487 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 1411 5.1 %RANDOM
Rwork0.2076 ---
obs0.2092 27787 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.39 Å2 / Biso mean: 20.4499 Å2 / Biso min: 8.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.42 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 54 308 2515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192266
X-RAY DIFFRACTIONr_bond_other_d0.0010.022125
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9853079
X-RAY DIFFRACTIONr_angle_other_deg0.78434869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0923.592103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13215362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2551518
X-RAY DIFFRACTIONr_chiral_restr0.0750.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212568
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02520
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 108 -
Rwork0.301 1847 -
all-1955 -
obs--95.32 %
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)
10.9303-0.0101-0.10060.70670.2210.7751-0.0562-0.1217-0.14230.084-0.00080.04220.08690.07530.05710.07410.00880.02290.07740.03480.060815.720218.99144.4848
26.1386-0.33060.20774.8901-0.06314.42040.041-0.4257-0.21620.4076-0.00460.22030.1661-0.1668-0.03640.1258-0.01720.04250.150.03820.03139.831920.097616.1945
32.2176-0.1528-0.92431.0972-0.02880.9984-0.111-0.1686-0.20680.01690.0525-0.05790.0440.09820.05850.08120.00560.00310.08370.02830.030722.172818.20114.1507
40.96820.0488-0.40860.61490.21611.15010.0525-0.01270.0578-0.07320.01610.0041-0.25310.0737-0.06860.1216-0.02890.01550.0390.00270.049318.269739.4511-6.3288
510.68155.35393.302914.04411.56396.7532-0.04280.4230.9022-0.2615-0.0739-0.0525-0.4319-0.06820.11670.10780.02280.05440.03560.04250.162412.765751.438-1.6367
61.0850.3581-0.09861.79480.54941.6460.03680.02720.1222-0.01050.0586-0.0332-0.17750.0326-0.09540.08350.01110.02280.01760.00570.051114.904639.7411-7.9461
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 83
2X-RAY DIFFRACTION2A84 - 109
3X-RAY DIFFRACTION3A110 - 141
4X-RAY DIFFRACTION4B2 - 86
5X-RAY DIFFRACTION5B87 - 99
6X-RAY DIFFRACTION6B100 - 141

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