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- PDB-4jsy: Structure of Clostridium thermocellum polynucleotide kinase bound... -

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Basic information

Entry
Database: PDB / ID: 4jsy
TitleStructure of Clostridium thermocellum polynucleotide kinase bound to GTP
ComponentsMetallophosphoesterase
KeywordsTRANSFERASE / RNA repair / P-Loop phosphotransferase / polynucleotide kinase
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
GUANOSINE-5'-TRIPHOSPHATE / Metallophosphoesterase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Direct refinement / Resolution: 2.14 Å
AuthorsDas, U. / Wang, L.K. / Smith, P. / Shuman, S.
CitationJournal: Biochemistry / Year: 2013
Title: Structural and biochemical analysis of the phosphate donor specificity of the polynucleotide kinase component of the bacterial pnkphen1 RNA repair system.
Authors: Das, U. / Wang, L.K. / Smith, P. / Shuman, S.
History
DepositionMar 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Oct 16, 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_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.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

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Assembly

Deposited unit
A: Metallophosphoesterase
B: Metallophosphoesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4176
Polymers39,3222
Non-polymers1,0954
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-35 kcal/mol
Surface area16560 Å2
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

#1: Protein Metallophosphoesterase


Mass: 19661.062 Da / Num. of mol.: 2 / Mutation: V44M, 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
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, 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


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100mM sodium citrate, 5mM DTT, 100mM MgCl2, 16-18% PEG 3350, 2mM GTP, 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: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.14→39.6 Å / Num. all: 20889 / Num. obs: 20889 / % possible obs: 100 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -999
Reflection shellResolution: 2.14→2.26 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: Direct refinement / Resolution: 2.14→37.492 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 1642 7.88 %random
Rwork0.1675 ---
obs0.1705 20830 98.32 %-
all-20871 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.14→37.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 66 180 2980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052871
X-RAY DIFFRACTIONf_angle_d0.9963890
X-RAY DIFFRACTIONf_dihedral_angle_d15.5631114
X-RAY DIFFRACTIONf_chiral_restr0.059439
X-RAY DIFFRACTIONf_plane_restr0.004490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.18550.19761040.16481270X-RAY DIFFRACTION80
2.1855-2.2560.22291380.16091608X-RAY DIFFRACTION100
2.256-2.33670.22341360.16361574X-RAY DIFFRACTION100
2.3367-2.43020.251370.17551594X-RAY DIFFRACTION100
2.4302-2.54080.22731390.1721615X-RAY DIFFRACTION100
2.5408-2.67470.22631390.18531624X-RAY DIFFRACTION100
2.6747-2.84220.22531390.17611601X-RAY DIFFRACTION100
2.8422-3.06160.20821370.18851615X-RAY DIFFRACTION100
3.0616-3.36950.22631390.17981624X-RAY DIFFRACTION100
3.3695-3.85670.18431420.16561649X-RAY DIFFRACTION100
3.8567-4.85730.17121420.1431652X-RAY DIFFRACTION100
4.8573-37.4980.19211500.1651762X-RAY DIFFRACTION100

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