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- PDB-4gp6: Polynucleotide kinase -

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Basic information

Entry
Database: PDB / ID: 4gp6
TitlePolynucleotide kinase
ComponentsMetallophosphoesterase
KeywordsTRANSFERASE / polynucleotide kinase phosphatase / RNA repair
Function / homology
Function and homology information


hydrolase activity / carbohydrate metabolic process / GTP binding / ATP binding / metal ion binding
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 / P-loop containing nucleotide triphosphate hydrolases ...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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Metallophosphoesterase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Feb 28, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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)39,8446
Polymers38,9412
Non-polymers9034
Water4,270237
1
A: Metallophosphoesterase
hetero molecules

B: Metallophosphoesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8446
Polymers38,9412
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+5/2,-y,z+1/21
Buried area3330 Å2
ΔGint-42 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.690, 71.560, 118.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Metallophosphoesterase


Mass: 19470.275 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, 200mM MgCl2, 30% PEG 400, 2mM ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→45.6 Å / Num. all: 22461 / Num. obs: 22214 / % possible obs: 98.9 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.1→2.21 Å / % possible all: 92.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→35.78 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 1740 7.85 %random
Rwork0.1769 ---
obs0.181 22154 98.84 %-
all-22414 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.693 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.8629 Å20 Å20 Å2
2--6.7078 Å20 Å2
3----12.5707 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2729 0 56 237 3022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072851
X-RAY DIFFRACTIONf_angle_d1.0953863
X-RAY DIFFRACTIONf_dihedral_angle_d15.7291099
X-RAY DIFFRACTIONf_chiral_restr0.064443
X-RAY DIFFRACTIONf_plane_restr0.004488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16180.27481210.20911505X-RAY DIFFRACTION89
2.1618-2.23160.28981540.191630X-RAY DIFFRACTION97
2.2316-2.31130.27661330.19231698X-RAY DIFFRACTION100
2.3113-2.40390.30491280.1841699X-RAY DIFFRACTION100
2.4039-2.51330.23851590.18711677X-RAY DIFFRACTION100
2.5133-2.64570.2431430.19121710X-RAY DIFFRACTION100
2.6457-2.81140.29211410.19341722X-RAY DIFFRACTION100
2.8114-3.02840.24541530.18181700X-RAY DIFFRACTION100
3.0284-3.33290.24011590.1791712X-RAY DIFFRACTION100
3.3329-3.81480.2031450.16961743X-RAY DIFFRACTION100
3.8148-4.80440.17221450.14061761X-RAY DIFFRACTION100
4.8044-35.78520.19581590.18411857X-RAY DIFFRACTION100

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