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- PDB-1f3f: STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHO... -

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Basic information

Entry
Database: PDB / ID: 1f3f
TitleSTRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHOSPHATE.MG COMPLEX
ComponentsPROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)
KeywordsTRANSFERASE / NUCLEOSIDE DIPHOSPHATE KINASE / ANTI-HIV NUCLEOSIDE ANALOGUE / PHOSPHORYLATION / CH...O BOND
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 / negative regulation of pinocytosis / nucleoside triphosphate biosynthetic process / 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 / negative regulation of pinocytosis / nucleoside triphosphate biosynthetic process / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / negative regulation of exocytosis / GTP biosynthetic process / negative regulation of phagocytosis / nucleoside diphosphate kinase activity / translational elongation / phagocytic vesicle / secretory granule / response to bacterium / actin cytoskeleton organization / cytoskeleton / ribosome / G protein-coupled receptor signaling pathway / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase (NDPK)-like domain profile. / 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 ...Nucleoside diphosphate kinase (NDPK)-like domain profile. / 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-D4D / Chem-D4T / PHOSPHATE ION / Nucleoside diphosphate kinase, cytosolic
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsMeyer, P. / Schneider, B. / Sarfati, S. / Deville-Bonne, D. / Guerreiro, C. / Boretto, J. / Janin, J. / Veron, M. / Canard, B.
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 2, 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 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)52,15011
Polymers50,2063
Non-polymers1,9458
Water6,197344
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)104,30022
Polymers100,4116
Non-polymers3,88916
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area20270 Å2
ΔGint-129 kcal/mol
Surface area32280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.018, 70.018, 152.098
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 16735.242 Da / Num. of mol.: 3 / Mutation: H122G
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

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Non-polymers , 5 types, 352 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-D4T / 2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-TRIPHOSPHATE


Mass: 464.153 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N2O13P3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-D4D / 2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-DIPHOSPHATE


Mass: 384.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O10P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
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
119 %PEG4001drop
250 mMTris-HCl1drop
320 mM1dropMgCl2
46 mg/mlprotein1drop
57.5 mMd4T triphosphate1drop
638 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.364
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.364 Å / Relative weight: 1
ReflectionResolution: 1.85→29.73 Å / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.071
Reflection shellResolution: 1.85→1.97 Å / Rmerge(I) obs: 0.328 / % possible all: 98.7
Reflection
*PLUS
Num. obs: 37405 / % possible obs: 99.3 % / Rmerge(I) obs: 0.056

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.85→29.73 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1504 4 %RANDOM
Rwork0.203 ---
obs0.203 37405 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.4 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0.02 Å20 Å2
2---0.39 Å20 Å2
3---0.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 116 344 3883
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.762
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.662.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 207 3.4 %
Rwork0.233 5892 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2D4T_DNA-RNA_REP.PARAMD4T_DNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5D4D_DNA-RNA.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 35535
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04
LS refinement shell
*PLUS
Rfactor Rfree: 0.287 / Rfactor Rwork: 0.233

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