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- PDB-4qbn: VRR_NUC domain -

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Basic information

Entry
Database: PDB / ID: 4qbn
TitleVRR_NUC domain
ComponentsNuclease
KeywordsHYDROLASE / Nuclease
Function / homology
Function and homology information


nuclease activity / nucleic acid binding
Similarity search - Function
VRR-NUC domain / VRR-NUC domain / VRR_NUC / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
VRR-NUC domain-containing protein
Similarity search - Component
Biological speciesSalmonella phage SETP3 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSmerdon, S.J. / Pennell, S. / Li, J.
CitationJournal: Cell Rep / Year: 2014
Title: FAN1 activity on asymmetric repair intermediates is mediated by an atypical monomeric virus-type replication-repair nuclease domain.
Authors: Pennell, S. / Declais, A.C. / Li, J. / Haire, L.F. / Berg, W. / Saldanha, J.W. / Taylor, I.A. / Rouse, J. / Lilley, D.M. / Smerdon, S.J.
History
DepositionMay 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Nuclease
B: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2738
Polymers21,6972
Non-polymers5766
Water1,76598
1
A: Nuclease
hetero molecules

A: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2738
Polymers21,6972
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_655-x+3/2,-y+1/2,z1
Buried area3140 Å2
ΔGint-82 kcal/mol
Surface area10190 Å2
MethodPISA
2
B: Nuclease
hetero molecules

B: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2738
Polymers21,6972
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y+1/2,-z+1/21
Buried area3010 Å2
ΔGint-68 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.221, 99.329, 109.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-228-

HOH

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Components

#1: Protein Nuclease


Mass: 10848.489 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage SETP3 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A3EZR7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.2M ammonium sulphate, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL
RadiationMonochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 20375 / Num. obs: 20335 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→19.773 Å / SU ML: 0.16 / σ(F): 1.37 / Phase error: 21.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1972 1037 5.13 %
Rwork0.1634 --
obs0.1651 20234 99.73 %
all-20242 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→19.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1534 0 30 98 1662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181592
X-RAY DIFFRACTIONf_angle_d1.6772138
X-RAY DIFFRACTIONf_dihedral_angle_d13.443608
X-RAY DIFFRACTIONf_chiral_restr0.134216
X-RAY DIFFRACTIONf_plane_restr0.009272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.94750.25121620.19852689X-RAY DIFFRACTION99
1.9475-2.06940.24261400.16862733X-RAY DIFFRACTION100
2.0694-2.22890.20541290.15532719X-RAY DIFFRACTION100
2.2289-2.45290.24221380.16712729X-RAY DIFFRACTION100
2.4529-2.8070.20461630.17482734X-RAY DIFFRACTION100
2.807-3.53320.17631460.15982776X-RAY DIFFRACTION100
3.5332-19.77430.18221590.15812817X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.3467-1.9649-5.56581.61840.99116.64720.10711.3634-0.702-0.1273-0.109-0.17210.5393-1.0365-0.07530.43040.0234-0.03980.2743-0.12850.368867.01517.153.5618
29.6225.131-4.72298.7456-4.90213.27840.53130.44340.164-0.1833-0.4807-0.085-0.20590.6108-0.09220.370.00910.00180.4188-0.00590.262366.388222.30880.272
35.9413-1.2064-1.2484.23150.51973.49240.17640.1343-0.4136-0.172-0.0041-0.36430.33440.48390.01440.23010.0485-0.01290.2126-0.0570.237171.812215.736.9086
47.8915-3.8895-4.44715.80872.40893.07010.03330.63460.4661-0.53070.1193-0.605-0.34650.8617-0.15920.2005-0.02880.02910.3386-0.01420.310778.316526.18815.2463
53.7630.8492-0.063.89860.95223.98420.2207-0.1278-0.53420.2591-0.1948-0.25010.72480.2230.07870.28730.05-0.06080.161-0.00550.22573.291912.295812.4854
63.60911.6173-2.49872.3299-1.42562.7779-0.35610.02620.0636-0.14080.5104-0.54-1.00661.7102-0.21750.4185-0.46750.04510.5901-0.08720.345589.104642.695224.8222
74.9142-1.6865-3.86275.51021.9697.3170.01640.42610.0853-0.29720.1053-0.59170.00781.0252-0.16470.2248-0.06130.0160.5202-0.04940.198988.365828.801727.0779
81.88020.0841-0.17073.6441-0.07082.89150.06210.15310.1415-0.39560.0577-0.2544-0.32920.6555-0.07870.2569-0.10930.03510.3895-0.03480.215884.362932.820716.5447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 65 )
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 77 )
5X-RAY DIFFRACTION5chain 'A' and (resid 78 through 94 )
6X-RAY DIFFRACTION6chain 'B' and (resid 7 through 24 )
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 49 )
8X-RAY DIFFRACTION8chain 'B' and (resid 50 through 94 )

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