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- PDB-3b54: Saccharomyces cerevisiae nucleoside diphosphate kinase -

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Basic information

Entry
Database: PDB / ID: 3b54
TitleSaccharomyces cerevisiae nucleoside diphosphate kinase
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / ALPHA/BETA sandwich / ATP-binding / Kinase / Magnesium / Metal-binding / Mitochondrion / Nucleotide metabolism / Nucleotide-binding / Phosphorylation
Function / homology
Function and homology information


: / nucleoside triphosphate biosynthetic process / Interconversion of nucleotide di- and triphosphates / nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / Neutrophil degranulation / mitochondrial intermembrane space ...: / nucleoside triphosphate biosynthetic process / Interconversion of nucleotide di- and triphosphates / nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / Neutrophil degranulation / mitochondrial intermembrane space / DNA repair / DNA damage response / mitochondrion / ATP binding / metal ion binding / cytosol
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
PHOSPHATE ION / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MIR / Resolution: 3.1 Å
AuthorsWang, H.B. / Bao, R. / Cheng, Y.X.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of Ynk1 from the yeast Saccharomyces cerevisiae
Authors: Wang, H. / Bao, R. / Jiang, C. / Yang, Z. / Zhou, C.-Z. / Chen, Y.
History
DepositionOct 25, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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)36,6084
Polymers36,4182
Non-polymers1902
Water1267
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)109,82312
Polymers109,2536
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area18130 Å2
ΔGint-102 kcal/mol
Surface area34210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.920, 185.920, 185.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 2 - 153 / Label seq-ID: 10 - 161

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Nucleoside diphosphate kinase / NDK / NDP kinase


Mass: 18208.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NDK1, YNK, YNK1 / Plasmid: pET28a-derived expression vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36010, nucleoside-diphosphate kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.68 Å3/Da / Density % sol: 66.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.6
Details: 13% isopropanol, 19% TBA(tert-butyl alcohol), 0.1M Na Citrate pH 5.6, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54179
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 3→29.4 Å / Num. all: 10547 / Num. obs: 10547 / % possible obs: 98.2 % / Redundancy: 6.41 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 5.6122
Reflection shellResolution: 3→3.16 Å / Redundancy: 4.89 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.1 / % possible all: 93.35

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1nue

1nue


Resolution: 3.1→15 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.891 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26081 431 4.6 %RANDOM
Rwork0.23081 ---
obs0.23221 8869 95.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60 Å2
Refinement stepCycle: LAST / Resolution: 3.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 10 7 2307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222342
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.9583154
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4225286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.51624.038104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.91615428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5291516
X-RAY DIFFRACTIONr_chiral_restr0.1140.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021732
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2550.21091
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3330.21563
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3150.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4381.51430
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80222296
X-RAY DIFFRACTIONr_scbond_it1.2923912
X-RAY DIFFRACTIONr_scangle_it2.1224.5858
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1145 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.030.05
tight thermal0.040.5
LS refinement shellResolution: 3.1→3.177 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 37 -
Rwork0.279 597 -
obs--93.24 %
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)
16.6768-0.98-1.90892.9465-0.26065.1058-0.3028-0.3463-1.57-0.04260.24010.37261.0141-0.45960.0627-0.1625-0.2353-0.044-0.28580.00450.137317.52792.822329.8158
27.322-2.1411-1.30765.4123-0.27293.2058-0.2656-1.5432-0.351.08390.0678-0.4343-0.04380.36190.1978-0.1752-0.0434-0.24140.12930.0066-0.286328.958716.667543.6547
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 15310 - 161
2X-RAY DIFFRACTION1AC1541
3X-RAY DIFFRACTION2BB2 - 15310 - 161
4X-RAY DIFFRACTION2BD1541

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