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- PDB-4qm6: Structure of bacterial polynucleotide kinase bound to GTP and RNA -

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Basic information

Entry
Database: PDB / ID: 4qm6
TitleStructure of bacterial polynucleotide kinase bound to GTP and RNA
Components
  • Metallophosphoesterase
  • RNA
KeywordsTRANSFERASE/RNA / RNA repair / P-loop phosphotransferase / polynucleotide kinase / HYDROLASE-RNA complex / TRANSFERASE-RNA complex
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
GUANOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / RNA / Metallophosphoesterase
Similarity search - Component
Biological speciesRuminiclostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular refinement / Resolution: 1.5 Å
AuthorsDas, U. / Wang, L.K. / Smith, P. / Shuman, S.
CitationJournal: J.Bacteriol. / Year: 2014
Title: Structures of bacterial polynucleotide kinase in a michaelis complex with nucleoside triphosphate (NTP)-Mg2+ and 5'-OH RNA and a mixed substrate-product complex with NTP-Mg2+ and a 5'- ...Title: Structures of bacterial polynucleotide kinase in a michaelis complex with nucleoside triphosphate (NTP)-Mg2+ and 5'-OH RNA and a mixed substrate-product complex with NTP-Mg2+ and a 5'-phosphorylated oligonucleotide.
Authors: Das, U. / Wang, L.K. / Smith, P. / Munir, A. / Shuman, S.
History
DepositionJun 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: 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_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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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
C: RNA
D: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,32514
Polymers42,0214
Non-polymers1,30510
Water10,215567
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.310, 74.420, 119.620
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 / RNA chain , 2 types, 4 molecules ABCD

#1: Protein Metallophosphoesterase


Mass: 19487.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium thermocellum (bacteria)
Strain: ATCC 27405 / DSM 1237 / Gene: Cthe_2768 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DJ38
#2: RNA chain RNA /


Mass: 1522.944 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYNTHETIC POLYNUCLEOTIDE

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Non-polymers , 5 types, 577 molecules

#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM sodium citrate, 100 mM magnesium chloride, 18-24% PEG 6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→39.9 Å / Num. all: 75553 / Num. obs: 75553 / % possible obs: 100 % / Observed criterion σ(F): 9999 / Observed criterion σ(I): 3
Reflection shellResolution: 1.5→1.58 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: molecular refinement / Resolution: 1.5→39.375 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 16.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.175 5910 7.83 %random
Rwork0.1531 ---
obs0.1548 75454 99.95 %-
all-75529 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→39.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 168 76 567 3548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073120
X-RAY DIFFRACTIONf_angle_d1.1954276
X-RAY DIFFRACTIONf_dihedral_angle_d18.4561245
X-RAY DIFFRACTIONf_chiral_restr0.074489
X-RAY DIFFRACTIONf_plane_restr0.006512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51710.20292260.16532229X-RAY DIFFRACTION100
1.5171-1.53490.17411810.16112303X-RAY DIFFRACTION100
1.5349-1.55360.1661970.14982262X-RAY DIFFRACTION100
1.5536-1.57330.17021900.14192296X-RAY DIFFRACTION100
1.5733-1.5940.19241930.14142305X-RAY DIFFRACTION100
1.594-1.61580.14811710.13842302X-RAY DIFFRACTION100
1.6158-1.63890.16832020.13962300X-RAY DIFFRACTION100
1.6389-1.66340.16292130.13762252X-RAY DIFFRACTION100
1.6634-1.68940.17571720.14832377X-RAY DIFFRACTION100
1.6894-1.71710.18242020.14682250X-RAY DIFFRACTION100
1.7171-1.74670.18121890.14832301X-RAY DIFFRACTION100
1.7467-1.77840.18482140.15312254X-RAY DIFFRACTION100
1.7784-1.81260.17962050.15142335X-RAY DIFFRACTION100
1.8126-1.84960.16621830.15142292X-RAY DIFFRACTION100
1.8496-1.88990.1761880.14782298X-RAY DIFFRACTION100
1.8899-1.93380.16042070.15122303X-RAY DIFFRACTION100
1.9338-1.98220.18911980.14992302X-RAY DIFFRACTION100
1.9822-2.03580.16521960.15532307X-RAY DIFFRACTION100
2.0358-2.09570.16631720.1552345X-RAY DIFFRACTION100
2.0957-2.16330.16821830.1452316X-RAY DIFFRACTION100
2.1633-2.24060.16142160.15042299X-RAY DIFFRACTION100
2.2406-2.33030.17132010.15182323X-RAY DIFFRACTION100
2.3303-2.43640.16821750.14912342X-RAY DIFFRACTION100
2.4364-2.56480.17852200.15542317X-RAY DIFFRACTION100
2.5648-2.72540.17951930.16382341X-RAY DIFFRACTION100
2.7254-2.93580.18742170.15892331X-RAY DIFFRACTION100
2.9358-3.23110.16631800.15952370X-RAY DIFFRACTION100
3.2311-3.69840.16792060.15682372X-RAY DIFFRACTION100
3.6984-4.65840.17082060.13842397X-RAY DIFFRACTION100
4.6584-39.38860.20012140.17142523X-RAY DIFFRACTION100

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