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- PDB-3ty9: Crystal Structure of C. Thermocellum PNKP Ligase Domain AMP-Adenylate -

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Basic information

Entry
Database: PDB / ID: 3ty9
TitleCrystal Structure of C. Thermocellum PNKP Ligase Domain AMP-Adenylate
ComponentsPolynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase
KeywordsTRANSFERASE / DNA ligase/mRNA capping enzyme / RNA Ligase / Adenylyltransferase / HEN1
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 / DNA ligase/mRNA capping enzyme / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type ...: / Polynucleotide kinase-phosphatase, bacterial / PrpE-like, metallophosphatase domain / Polynucleotide kinase-phosphatase, ligase domain / PNKP adenylyltransferase domain, ligase domain / : / AAA domain / DNA ligase/mRNA capping enzyme / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / D-amino Acid Aminotransferase; Chain A, domain 1 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Metallophosphoesterase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsSmith, P. / Wang, L. / Shuman, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family.
Authors: Smith, P. / Wang, L.K. / Nair, P.A. / Shuman, S.
History
DepositionSep 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_conn_type.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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase
B: Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase
C: Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase
D: Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,87229
Polymers180,4034
Non-polymers3,46925
Water93752
1
A: Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase
hetero molecules

C: Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,98215
Polymers90,2012
Non-polymers1,78113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area7000 Å2
ΔGint-96 kcal/mol
Surface area31890 Å2
MethodPISA
2
A: Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase
B: Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,10016
Polymers90,2012
Non-polymers1,89914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-109 kcal/mol
Surface area32380 Å2
MethodPISA
3
B: Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase
hetero molecules

D: Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,89014
Polymers90,2012
Non-polymers1,68812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area6720 Å2
ΔGint-106 kcal/mol
Surface area31820 Å2
MethodPISA
4
C: Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase
D: Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,77213
Polymers90,2012
Non-polymers1,57011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-105 kcal/mol
Surface area33480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.500, 132.760, 162.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsPROTEIN IS KNOWN TO FORM A DIMER WHICH INTERACTS WITH A DIMER OF HEN1 TO GIVE A HETEREOTETRAMER (2-PNKP/2-HEN1). THE OLIGOMERIC ORGANIZATIONS PRESENT IN THE CRYSTAL ARE ENUMERATED BELOW BUT MAY NOT CORRESPOND TO ANY OLIGOMER PRESENT IN THE HEN1/PNKP HETERODIMER

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase


Mass: 45100.680 Da / Num. of mol.: 4 / Fragment: Nucleotide Ligase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / Gene: Cthe_2768 / Plasmid: pET28b-smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3DJ38, RNA ligase (ATP)

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Non-polymers , 6 types, 77 molecules

#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: HEPES buffer 20% (v/v) Hexylene Glycol, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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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: Feb 15, 2011 / Details: See Beamline Documentation
RadiationMonochromator: See Beamline Documentation / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.12→50 Å / Num. all: 37602 / Num. obs: 37527 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rsym value: 0.065 / Net I/σ(I): 9.2

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3TY5

3ty5


Resolution: 3.12→41.185 Å / SU ML: 0.38 / σ(F): 1.38 / Phase error: 31.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 1669 4.46 %random
Rwork0.2189 ---
obs0.221 37457 99.78 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.301 Å2 / ksol: 0.263 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-51.8235 Å2-0 Å2-0 Å2
2---22.0948 Å2-0 Å2
3----21.6232 Å2
Refinement stepCycle: LAST / Resolution: 3.12→41.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12022 0 226 52 12300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512490
X-RAY DIFFRACTIONf_angle_d0.85116886
X-RAY DIFFRACTIONf_dihedral_angle_d15.1744651
X-RAY DIFFRACTIONf_chiral_restr0.0591836
X-RAY DIFFRACTIONf_plane_restr0.0032132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.21180.41491360.37592941X-RAY DIFFRACTION100
3.2118-3.31540.3731380.34432948X-RAY DIFFRACTION100
3.3154-3.43390.36651380.3052940X-RAY DIFFRACTION100
3.4339-3.57130.33151380.27112945X-RAY DIFFRACTION100
3.5713-3.73370.30131360.24322933X-RAY DIFFRACTION100
3.7337-3.93040.27371390.23062962X-RAY DIFFRACTION100
3.9304-4.17640.27851390.20732985X-RAY DIFFRACTION100
4.1764-4.49850.25771370.17052965X-RAY DIFFRACTION100
4.4985-4.95060.18661390.15312989X-RAY DIFFRACTION100
4.9506-5.66530.22091400.17692995X-RAY DIFFRACTION100
5.6653-7.13170.28371420.2263034X-RAY DIFFRACTION100
7.1317-41.18820.22111470.19863151X-RAY DIFFRACTION99

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