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- PDB-3ngr: Crystal structure of Leishmania nucleoside diphosphate kinase b w... -

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Basic information

Entry
Database: PDB / ID: 3ngr
TitleCrystal structure of Leishmania nucleoside diphosphate kinase b with unordered nucleotide-binding loop.
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / NDKb / phosphate ion
Function / homology
Function and homology information


nucleoside-diphosphate kinase / ciliary plasm / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP 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
PHOSPHATE ION / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsTrindade, D.M. / Sousa, T.A.C.B. / Tonoli, C.C.C. / Santos, C.R. / Arni, R.K. / Ward, R.J. / Oliveira, A.H.C. / Murakami, M.T.
CitationJournal: Mol Biosyst / Year: 2011
Title: Molecular adaptability of nucleoside diphosphate kinase b from trypanosomatid parasites: stability, oligomerization and structural determinants of nucleotide binding.
Authors: Souza, T.A. / Trindade, D.M. / Tonoli, C.C. / Santos, C.R. / Ward, R.J. / Arni, R.K. / Oliveira, A.H. / Murakami, M.T.
History
DepositionJun 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2013Group: Structure summary
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7562
Polymers16,6611
Non-polymers951
Water30617
1
A: Nucleoside diphosphate kinase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)100,53612
Polymers99,9666
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_545x,x-y-1,-z+1/21
Buried area11990 Å2
ΔGint-102 kcal/mol
Surface area32370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.769, 120.769, 64.892
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Nucleoside diphosphate kinase


Mass: 16660.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: L1648.07, LmjF32.2950, NDKb / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9U1E1, nucleoside-diphosphate kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 4.1 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: sodium/potassium phosphate, pH pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
PH range: pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2010
RadiationMonochromator: silicon double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 2.95→104.59 Å / Num. obs: 6148 / % possible obs: 98 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.086
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 7 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 4.5 / % possible all: 86.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry: 1NSK

1nsk


Resolution: 2.95→104.59 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.834 / SU B: 18.685 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R: 0.489 / ESU R Free: 0.417 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3505 284 4.6 %RANDOM
Rwork0.25288 ---
obs0.25731 5850 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 63.55 Å2
Baniso -1Baniso -2Baniso -3
1-3.9 Å21.95 Å20 Å2
2--3.9 Å20 Å2
3----5.84 Å2
Refinement stepCycle: LAST / Resolution: 2.95→104.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms896 0 5 17 918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.022908
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5721.9431227
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4255115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85823.07739
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.89815149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.341158
X-RAY DIFFRACTIONr_chiral_restr0.1430.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021681
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3141.5575
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5022919
X-RAY DIFFRACTIONr_scbond_it3.3513333
X-RAY DIFFRACTIONr_scangle_it5.744.5308
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.615 19 -
Rwork0.355 352 -
obs--84.51 %

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