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- PDB-5yol: Crystal structure of octameric form of Nucleoside diphosphate kin... -

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Entry
Database: PDB / ID: 5yol
TitleCrystal structure of octameric form of Nucleoside diphosphate kinase from Acinetobacter baumannii at 2.2 A resolution
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE
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 speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSingh, P.K. / Sikarwar, J. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of octameric form of Nucleoside diphosphate kinase from Acinetobacter baumannii at 2.2 A resolution
Authors: Singh, P.K. / Sikarwar, J. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionOct 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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_ncs_dom_lim
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.ptnr1_symmetry / _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.ptnr2_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,15920
Polymers123,8688
Non-polymers29212
Water9,008500
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15760 Å2
ΔGint-146 kcal/mol
Surface area47140 Å2
Unit cell
Length a, b, c (Å)70.100, 69.930, 71.700
Angle α, β, γ (deg.)80.51, 69.94, 89.76
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 1 - 143 / Label seq-ID: 1 - 143

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18BB
28CC
19BB
29DD
110BB
210EE
111BB
211FF
112BB
212GG
113BB
213HH
114CC
214DD
115CC
215EE
116CC
216FF
117CC
217GG
118CC
218HH
119DD
219EE
120DD
220FF
121DD
221GG
122DD
222HH
123EE
223FF
124EE
224GG
125EE
225HH
126FF
226GG
127FF
227HH
128GG
228HH

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

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


Mass: 15483.479 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: ndk, A7A59_04275, A7M79_04705, A7M90_00500, A7N09_02655, AB895_2022, AB988_1826, AB994_3665, ABUW_3381, APD06_17770, AZE33_02560, B4R90_00300, B9X91_01430, B9X95_00285, BGC29_14850, CAS83_ ...Gene: ndk, A7A59_04275, A7M79_04705, A7M90_00500, A7N09_02655, AB895_2022, AB988_1826, AB994_3665, ABUW_3381, APD06_17770, AZE33_02560, B4R90_00300, B9X91_01430, B9X95_00285, BGC29_14850, CAS83_00635, CAS84_07305, CAT05_09960, CAT56_03875, CAT78_05970, CBE85_04645, CBI29_00577, IX87_17090, LV38_00051, NT90_02330
Production host: Escherichia coli (E. coli) / References: UniProt: V5VIC4, nucleoside-diphosphate kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES: 7.5, PEG400, 0.1MgCl2 / PH range: 5-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 5, 2017 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.2→66.322 Å / Num. obs: 56966 / % possible obs: 89.3 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.239 Å / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2842 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S0M

4s0m


Resolution: 2.2→66.322 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 8.871 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.247 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 2739 4.8 %RANDOM
Rwork0.21281 ---
obs0.21502 54227 89.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.307 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0.09 Å20.86 Å2
2---0.9 Å20.34 Å2
3---1.76 Å2
Refinement stepCycle: 1 / Resolution: 2.2→66.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8704 0 12 500 9216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198864
X-RAY DIFFRACTIONr_bond_other_d0.0020.028312
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.94411960
X-RAY DIFFRACTIONr_angle_other_deg1.014319208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97851136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97523.725408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15151472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3091564
X-RAY DIFFRACTIONr_chiral_restr0.10.21336
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021856
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_it3.4634.064568
X-RAY DIFFRACTIONr_mcbond_other3.4624.064567
X-RAY DIFFRACTIONr_mcangle_it5.1626.0715696
X-RAY DIFFRACTIONr_mcangle_other5.1626.0715697
X-RAY DIFFRACTIONr_scbond_it4.4724.6114296
X-RAY DIFFRACTIONr_scbond_other4.4724.6114297
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9556.6946265
X-RAY DIFFRACTIONr_long_range_B_refined9.66477.49835991
X-RAY DIFFRACTIONr_long_range_B_other9.64377.45435714
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A87740.06
12B87740.06
21A86760.07
22C86760.07
31A87000.07
32D87000.07
41A87220.06
42E87220.06
51A86740.06
52F86740.06
61A86820.07
62G86820.07
71A87140.07
72H87140.07
81B87500.06
82C87500.06
91B87920.06
92D87920.06
101B87980.05
102E87980.05
111B87500.05
112F87500.05
121B87440.06
122G87440.06
131B87800.06
132H87800.06
141C87320.06
142D87320.06
151C87560.05
152E87560.05
161C87480.06
162F87480.06
171C87280.06
172G87280.06
181C87180.06
182H87180.06
191D87560.05
192E87560.05
201D87900.04
202F87900.04
211D87900.04
212G87900.04
221D87620.05
222H87620.05
231E87120.06
232F87120.06
241E87260.06
242G87260.06
251E88160.05
252H88160.05
261F87940.04
262G87940.04
271F87220.05
272H87220.05
281G87340.05
282H87340.05
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 219 -
Rwork0.32 3922 -
obs--87.34 %

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