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- PDB-4gp7: Polynucleotide kinase -

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Basic information

Entry
Database: PDB / ID: 4gp7
TitlePolynucleotide kinase
ComponentsMetallophosphoesterase
KeywordsTRANSFERASE / polynucleotide kinase phosphatase / RNA repair
Function / homology
Function and homology information


phosphatase activity / GTP binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Polynucleotide kinase-phosphatase, bacterial / PrpE-like, metallophosphatase domain / Polynucleotide kinase-phosphatase, ligase domain / PNKP adenylyltransferase domain, ligase domain / : / AAA domain / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like ...Polynucleotide kinase-phosphatase, bacterial / PrpE-like, metallophosphatase domain / Polynucleotide kinase-phosphatase, ligase domain / PNKP adenylyltransferase domain, ligase domain / : / AAA domain / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / CITRIC ACID / Metallophosphoesterase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsWang, L.K. / Das, U. / Smith, P. / Shuman, S.
CitationJournal: Rna / Year: 2012
Title: Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system.
Authors: Wang, L.K. / Das, U. / Smith, P. / Shuman, S.
History
DepositionAug 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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.ptnr2_auth_asym_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_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallophosphoesterase
B: Metallophosphoesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7308
Polymers39,4522
Non-polymers1,2786
Water3,387188
1
A: Metallophosphoesterase
hetero molecules

B: Metallophosphoesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7308
Polymers39,4522
Non-polymers1,2786
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+3/2,-y+1,z+1/21
Buried area3760 Å2
ΔGint-37 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.306, 66.781, 119.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallophosphoesterase


Mass: 19725.996 Da / Num. of mol.: 2 / Mutation: V44M, I93M, L137M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / DSM 1237 / Gene: Cthe_2768 / Production host: Escherichia coli (E. coli)
References: UniProt: A3DJ38, polynucleotide 5'-hydroxyl-kinase

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Non-polymers , 5 types, 194 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100mM sodium citrate, 5mM DTT, 100mM MgCl2, 16% PEG 3350, 2mM ATP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 25287 / % possible obs: 99.8 % / Observed criterion σ(I): -3
Reflection shellResolution: 2→2.03 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→44.538 Å / SU ML: 0.24 / σ(F): 0.21 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 1977 7.91 %random
Rwork0.1753 ---
obs0.1797 24992 98.83 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.401 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1328 Å20 Å2-0 Å2
2--0.8749 Å2-0 Å2
3----1.0077 Å2
Refinement stepCycle: LAST / Resolution: 2→44.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 78 188 3004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082899
X-RAY DIFFRACTIONf_angle_d1.2223937
X-RAY DIFFRACTIONf_dihedral_angle_d16.6381124
X-RAY DIFFRACTIONf_chiral_restr0.071437
X-RAY DIFFRACTIONf_plane_restr0.005494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04960.35191360.23461540X-RAY DIFFRACTION93
2.0496-2.1050.29581360.21031578X-RAY DIFFRACTION97
2.105-2.1670.25371400.19061608X-RAY DIFFRACTION98
2.167-2.23690.22881360.17531610X-RAY DIFFRACTION99
2.2369-2.31690.2771360.17181611X-RAY DIFFRACTION99
2.3169-2.40960.25491410.18661628X-RAY DIFFRACTION99
2.4096-2.51930.27641410.19371658X-RAY DIFFRACTION100
2.5193-2.65210.25481400.18551623X-RAY DIFFRACTION100
2.6521-2.81820.22291420.17681648X-RAY DIFFRACTION100
2.8182-3.03580.24141430.18471665X-RAY DIFFRACTION100
3.0358-3.34120.23661430.17791663X-RAY DIFFRACTION100
3.3412-3.82450.19791440.16761677X-RAY DIFFRACTION100
3.8245-4.81750.17581460.13411706X-RAY DIFFRACTION100
4.8175-44.54920.18071530.16611800X-RAY DIFFRACTION100

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