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- PDB-1f6t: STRUCTURE OF THE NUCLEOSIDE DIPHOSPHATE KINASE/ALPHA-BORANO(RP)-T... -

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Basic information

Entry
Database: PDB / ID: 1f6t
TitleSTRUCTURE OF THE NUCLEOSIDE DIPHOSPHATE KINASE/ALPHA-BORANO(RP)-TDP.MG COMPLEX
ComponentsPROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
KeywordsTRANSFERASE / NUCLEOSIDE DIPHOSPHATE KINASE / ANTI-HIV NUCLEOSIDE ANALOGUE / PHOSPHORYLATION / BORANOPHOSPHATE
Function / homology
Function and homology information


dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / nucleoside triphosphate biosynthetic process / negative regulation of pinocytosis / nucleoside-diphosphate kinase / UTP biosynthetic process ...dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / nucleoside triphosphate biosynthetic process / negative regulation of pinocytosis / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / negative regulation of exocytosis / negative regulation of phagocytosis / GTP biosynthetic process / nucleoside diphosphate kinase activity / translational elongation / phagocytic vesicle / secretory granule / response to bacterium / actin cytoskeleton organization / cytoskeleton / ribosome / G protein-coupled receptor signaling pathway / phosphorylation / ATP binding / metal ion binding / plasma membrane / 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
Chem-TBD / Nucleoside diphosphate kinase, cytosolic
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 1.92 Å
AuthorsGuerreiro, C. / Boretto, J. / Janin, J. / Veron, M. / Canard, B. / Schneider, B. / Sarfati, S. / Deville-Bonne, D.
CitationJournal: EMBO J. / Year: 2000
Title: Structural basis for activation of alpha-boranophosphate nucleotide analogues targeting drug-resistant reverse transcriptase.
Authors: Meyer, P. / Schneider, B. / Sarfati, S. / Deville-Bonne, D. / Guerreiro, C. / Boretto, J. / Janin, J. / Veron, M. / Canard, B.
History
DepositionJun 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_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.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.value / _struct_conn.pdbx_dist_value / _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.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_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: PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
B: PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
C: PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7229
Polymers50,4493
Non-polymers1,2736
Water6,792377
1
A: PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
B: PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
C: PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
hetero molecules

A: PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
B: PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
C: PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,44418
Polymers100,8986
Non-polymers2,54612
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area18160 Å2
ΔGint-122 kcal/mol
Surface area33600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.359, 70.359, 153.792
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE) / NDK / NDP KINASE


Mass: 16816.336 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Plasmid: PTZ18R / Production host: Escherichia coli (E. coli) / References: UniProt: P22887, nucleoside-diphosphate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TBD / 2*-DEOXY-THYMIDINE-5*-ALPHA BORANO DIPHOSPHATE (ISOMER RP)


Mass: 400.024 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H19BN2O10P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG550 mme1drop
250 mMTris-HCl1drop
325 mM1dropMgCl2
47.5 mg/mlprotein1drop
511 mMalpha-borano-TDP1drop
628 %PEG5501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.92→30 Å / Num. obs: 33469 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.105
Reflection shell
*PLUS
Rmerge(I) obs: 0.327

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.92→30 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1378 4.1 %RANDOM
Rwork0.228 ---
obs0.228 33430 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.58 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20.24 Å20 Å2
2---0.37 Å20 Å2
3---0.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.92→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3446 0 78 377 3901
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.641.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it2.32
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 1.92→2.04 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 200 4.2 %
Rwork0.337 4514 -
obs--83.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMBTDP_DNA-RNA.TOP
X-RAY DIFFRACTION3BTDP_DNA-RNA_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96
LS refinement shell
*PLUS
Rfactor Rfree: 0.394 / Rfactor Rwork: 0.337

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