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- PDB-5yih: Crystal structure of tetrameric Nucleoside diphosphate kinase at ... -

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Basic information

Entry
Database: PDB / ID: 5yih
TitleCrystal structure of tetrameric Nucleoside diphosphate kinase at 1.98 A resolution from Acinetobacter baumannii
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Kinase
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-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: 1.98 Å
AuthorsBairagya, H.R. / Sikarwar, J. / Iqbal, N. / Singh, P.K. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of tetrameric Nucleoside diphosphate kinase at 1.98 A resolution from Acinetobacter baumannii
Authors: Bairagya, H.R. / Sikarwar, J. / Iqbal, N. / Singh, P.K. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionOct 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.2Nov 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
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

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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
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0559
Polymers61,9344
Non-polymers1225
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-64 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.880, 70.470, 68.850
Angle α, β, γ (deg.)90.00, 109.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 15483.479 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81
Gene: ndk, F911_03401, HMPREF0010_01731 / Production host: Escherichia coli (E. coli) / References: UniProt: D0CAF1, nucleoside-diphosphate kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.69 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES: 7.5, PEG3350, 0.1MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.966 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 5, 2017 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.98→68.8 Å / Num. obs: 45707 / % possible obs: 98.7 % / Redundancy: 3 % / Net I/σ(I): 8.7
Reflection shellResolution: 1.98→2.009 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2261

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S0M

4s0m


Resolution: 1.98→68.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.085 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25571 2259 4.9 %RANDOM
Rwork0.2021 ---
obs0.20471 43447 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.989 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0.02 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.98→68.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4352 0 5 343 4700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194432
X-RAY DIFFRACTIONr_bond_other_d0.0020.024156
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9445980
X-RAY DIFFRACTIONr_angle_other_deg1.04739604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8545568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20823.725204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28415736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4541532
X-RAY DIFFRACTIONr_chiral_restr0.10.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025024
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02928
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_it3.3863.9932284
X-RAY DIFFRACTIONr_mcbond_other3.3473.9912283
X-RAY DIFFRACTIONr_mcangle_it4.8235.9652848
X-RAY DIFFRACTIONr_mcangle_other4.8265.9662849
X-RAY DIFFRACTIONr_scbond_it3.9954.4312148
X-RAY DIFFRACTIONr_scbond_other3.9944.4312149
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0896.463133
X-RAY DIFFRACTIONr_long_range_B_refined7.89948.5425030
X-RAY DIFFRACTIONr_long_range_B_other7.83948.3914958
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.975→2.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 168 -
Rwork0.313 3186 -
obs--98.79 %

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