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- PDB-4xru: Structure of Pnkp1/Rnl/Hen1 complex -

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Basic information

Entry
Database: PDB / ID: 4xru
TitleStructure of Pnkp1/Rnl/Hen1 complex
Components
  • Hen1
  • Pnkp1
  • Rnl
KeywordsPROTEIN BINDING / RNA repair / kinase / phosphatase / methyltransferase / ligase
Function / homology
Function and homology information


deoxynucleotide 3'-phosphatase activity / RNA methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / ATP binding / metal ion binding
Similarity search - Function
Polynucleotide kinase PNKP, C-terminal phosphatase domain / 3'-RNA ribose 2'-O-methyltransferase, Hen1 / Polynucleotide kinase-phosphatase, ligase domain / PNKP adenylyltransferase domain, ligase domain / AAA domain / HAD superfamily / HAD-like superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Uncharacterized protein / Polynucleotide kinase / Polynucleotide kinase-phosphatase ligase domain-containing protein
Similarity search - Component
Biological speciesCapnocytophaga gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.41 Å
AuthorsWang, P.
CitationJournal: Nat Commun / Year: 2015
Title: Reconstitution and structure of a bacterial Pnkp1-Rnl-Hen1 RNA repair complex.
Authors: Wang, P. / Selvadurai, K. / Huang, R.H.
History
DepositionJan 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pnkp1
B: Rnl
C: Hen1
D: Pnkp1
E: Rnl
F: Hen1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,58526
Polymers269,7876
Non-polymers3,79820
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24730 Å2
ΔGint-159 kcal/mol
Surface area97150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.483, 187.245, 111.999
Angle α, β, γ (deg.)90.00, 106.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Pnkp1


Mass: 36739.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capnocytophaga gingivalis (bacteria) / Strain: ATCC 33624 / Gene: CAPGI0001_2485 / Production host: Escherichia coli (E. coli) / References: UniProt: C2M8N3
#2: Protein Rnl


Mass: 46592.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capnocytophaga gingivalis (bacteria) / Strain: ATCC 33624 / Gene: CAPGI0001_2487 / Production host: Escherichia coli (E. coli) / References: UniProt: C2M8N4
#3: Protein Hen1


Mass: 51561.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capnocytophaga gingivalis (bacteria) / Strain: ATCC 33624 / Gene: CAPGI0001_1566 / Production host: Escherichia coli (E. coli) / References: UniProt: C2M7I7

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Non-polymers , 7 types, 112 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#9: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 4.9 Å3/Da / Density % sol: 74.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 65456 / % possible obs: 99.8 % / Redundancy: 5.1 % / Net I/σ(I): 13.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 3.41→42.93 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.38
RfactorNum. reflection% reflection
Rfree0.233 4285 3.78 %
Rwork0.176 --
obs0.179 56120 98.2 %
Displacement parametersBiso mean: 85.38 Å2
Refinement stepCycle: LAST / Resolution: 3.41→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15680 0 2941 92 18713
Refinement TLS params.Method: refined / Origin x: -27.2319 Å / Origin y: 4.919 Å / Origin z: -23.1882 Å
111213212223313233
T0.5456 Å2-0.1253 Å2-0.0453 Å2-0.4341 Å20.0243 Å2--0.5095 Å2
L0.4561 °2-0.5367 °2-0.0923 °2-0.6156 °20.0821 °2--0.0456 °2
S0.0821 Å °0.1088 Å °-0.0424 Å °0.0013 Å °-0.0897 Å °-0.015 Å °0.0006 Å °-0.0218 Å °0.0089 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 123
2X-RAY DIFFRACTION1allA142 - 312
3X-RAY DIFFRACTION1allA501
4X-RAY DIFFRACTION1allB1 - 394
5X-RAY DIFFRACTION1allB501
6X-RAY DIFFRACTION1allC1 - 377
7X-RAY DIFFRACTION1allC390 - 436
8X-RAY DIFFRACTION1allC501
9X-RAY DIFFRACTION1allD4 - 122
10X-RAY DIFFRACTION1allD145 - 312
11X-RAY DIFFRACTION1allD501
12X-RAY DIFFRACTION1allE2 - 394
13X-RAY DIFFRACTION1allE501
14X-RAY DIFFRACTION1allF1 - 377
15X-RAY DIFFRACTION1allF390 - 436
16X-RAY DIFFRACTION1allF501
17X-RAY DIFFRACTION1allL1 - 5
18X-RAY DIFFRACTION1allM1 - 6
19X-RAY DIFFRACTION1allS2 - 157
20X-RAY DIFFRACTION1allG1
21X-RAY DIFFRACTION1allG2 - 3
22X-RAY DIFFRACTION1allG4 - 5

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