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- PDB-4qbo: VRR_NUC domain -

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Basic information

Entry
Database: PDB / ID: 4qbo
TitleVRR_NUC domain
ComponentsNuclease
KeywordsHYDROLASE / nuclease
Function / homology
Function and homology information


nuclease activity / nucleic acid binding / metal ion 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 speciesStreptococcus phage P9 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 / 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.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_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: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4392
Polymers10,4151
Non-polymers241
Water2,792155
1
A: Nuclease
hetero molecules

A: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8794
Polymers20,8302
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2000 Å2
ΔGint-32 kcal/mol
Surface area10040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.854, 60.517, 81.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-344-

HOH

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Components

#1: Protein Nuclease


Mass: 10415.181 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus phage P9 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A7J283
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M sodium citrate, 20% w/v PEG3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 25, 2009
RadiationMonochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.3→15 Å / Num. all: 27534 / Num. obs: 27396 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→14.995 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 15.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1799 1378 5.04 %5%
Rwork0.1717 ---
obs0.1721 27354 99.46 %-
all-27502 --
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.587 Å2 / ksol: 0.473 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.1897 Å2-0 Å20 Å2
2---0.3406 Å20 Å2
3---2.5304 Å2
Refinement stepCycle: LAST / Resolution: 1.3→14.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms727 0 1 155 883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011842
X-RAY DIFFRACTIONf_angle_d1.2741139
X-RAY DIFFRACTIONf_dihedral_angle_d10.4341
X-RAY DIFFRACTIONf_chiral_restr0.068121
X-RAY DIFFRACTIONf_plane_restr0.007146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.34650.30721510.33072501X-RAY DIFFRACTION98
1.3465-1.40030.28371280.26692592X-RAY DIFFRACTION100
1.4003-1.4640.23281250.21422578X-RAY DIFFRACTION100
1.464-1.54110.21181320.16912584X-RAY DIFFRACTION100
1.5411-1.63760.18731420.15892607X-RAY DIFFRACTION100
1.6376-1.76380.16281410.15152576X-RAY DIFFRACTION100
1.7638-1.9410.17541290.14282624X-RAY DIFFRACTION100
1.941-2.22110.15741590.14682605X-RAY DIFFRACTION100
2.2211-2.79540.16781400.15172632X-RAY DIFFRACTION100
2.7954-14.99580.17431310.1852677X-RAY DIFFRACTION97
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)
14.13472.8867-1.12013.0886-0.68971.34460.04540.02530.08430.0479-0.02860.1371-0.0238-0.17960.00160.12850.00030.00910.1521-0.00120.09241.5103-11.798515.8916
21.8830.89561.73431.84481.32023.98140.1598-0.1288-0.11980.0021-0.0820.0780.1325-0.2832-0.07150.1371-0.0001-0.01540.14350.00990.13852.1846-3.43153.0173
36.37761.8321-1.29654.2321-0.86423.5959-0.0862-0.07050.13590.08810.0821-0.47270.0772-0.02080.04980.11580.0087-0.00640.079-0.01370.146710.9451-0.83956.6698
41.5140.39330.1620.60460.10191.22140.0739-0.1124-0.24780.1246-0.0348-0.08110.1291-0.1085-0.00820.1283-0.0168-0.00360.11620.01530.13434.7175-13.95254.4099
55.54484.0764-1.75713.3209-1.66761.0329-0.07340.0973-0.1096-0.21150.0694-0.1387-0.054-0.009-0.02520.1386-0.01440.00870.109-0.02560.12936.8187-12.168-6.7369
61.90210.615-1.16471.693-0.55452.5857-0.0231-0.13220.04460.02140.0266-0.09830.11440.15270.05120.09140.01750.00280.1047-0.0050.113914.0958-11.24548.9037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:19)
2X-RAY DIFFRACTION2chain 'A' and (resseq 20:37)
3X-RAY DIFFRACTION3chain 'A' and (resseq 38:44)
4X-RAY DIFFRACTION4chain 'A' and (resseq 45:59)
5X-RAY DIFFRACTION5chain 'A' and (resseq 60:72)
6X-RAY DIFFRACTION6chain 'A' and (resseq 73:90)

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