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- PDB-6oze: Crystal structure of the catalytic domain of human Endonuclease V... -

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Basic information

Entry
Database: PDB / ID: 6oze
TitleCrystal structure of the catalytic domain of human Endonuclease V (C140S/C225S/C226A/C228S)
ComponentsEndonuclease V
KeywordsHYDROLASE / Nucleic acid hydrolysis / RNA recognition / metal ion dependent catalysis / DNA damage / adenosine deamination
Function / homology
Function and homology information


DNA endonuclease activity, producing 5'-phosphomonoesters / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / cytoplasmic stress granule / single-stranded RNA binding / DNA repair / nucleolus / magnesium ion binding / DNA binding / cytoplasm
Similarity search - Function
Endonuclease V / Endonuclease V / archaeoglobus fulgidus dsm 4304 fold / archaeoglobus fulgidus dsm 4304 superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Endonuclease V
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSamara, N.L. / Yang, W.
CitationJournal: Mol.Cell / Year: 2019
Title: Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Authors: Wu, J. / Samara, N.L. / Kuraoka, I. / Yang, W.
History
DepositionMay 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 11, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5067
Polymers27,1571
Non-polymers3486
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-21 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.949, 50.949, 102.978
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Endonuclease V / hEndoV / Inosine-specific endoribonuclease


Mass: 27157.359 Da / Num. of mol.: 1 / Mutation: C140S/C225S/C226A/C228S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENDOV / Production host: Escherichia coli (E. coli)
References: UniProt: Q8N8Q3, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3.6 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 7, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→24.73 Å / Num. obs: 47096 / % possible obs: 98.2 % / Redundancy: 1 % / Biso Wilson estimate: 21.1 Å2 / Net I/σ(I): 9.9 / Num. measured all: 47096
Reflection shell
Resolution (Å)Redundancy (%)Num. measured allNum. unique obsDiffraction-IDNet I/σ(I) obs% possible all
1.5-1.521207320731288.3
8.21-24.731131131121.444.9

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2W35

2w35


Resolution: 1.5→24.729 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 22.84
RfactorNum. reflection% reflection
Rfree0.191 2240 4.76 %
Rwork0.1719 --
obs0.1729 47020 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.49 Å2 / Biso mean: 37.4917 Å2 / Biso min: 14.73 Å2
Refinement stepCycle: final / Resolution: 1.5→24.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 22 146 2076
Biso mean--57.87 48 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062088
X-RAY DIFFRACTIONf_angle_d0.8232853
X-RAY DIFFRACTIONf_chiral_restr0.079328
X-RAY DIFFRACTIONf_plane_restr0.005375
X-RAY DIFFRACTIONf_dihedral_angle_d21.283822
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.499-1.53160.29581160.28222515263189
1.5316-1.56720.26411100.25462767287796
1.5672-1.60640.256880.25229012989100
1.6064-1.64980.23531880.231727952983100
1.6498-1.69830.25161580.216828953053100
1.6983-1.75310.21761380.202628262964100
1.7531-1.81580.23271450.202628442989100
1.8158-1.88850.24211480.193228523000100
1.8885-1.97440.20861330.177128292962100
1.9744-2.07840.1991780.164628112989100
2.0784-2.20860.16251690.156128643033100
2.2086-2.3790.16971440.162728252969100
2.379-2.61810.20171160.167628682984100
2.6181-2.99640.21281400.182928953035100
2.9964-3.7730.1571470.147428122959100
3.773-24.73240.17911220.16062481260387
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)
13.7143-1.7459-3.60583.20921.70273.4534-0.0237-0.33450.63770.15280.25650.385-0.7966-0.1087-0.3020.53120.0678-0.00440.2489-0.01070.3381.60323.229311.1857
21.8420.4379-1.59842.27030.21516.20290.10790.17680.1029-0.02710.1529-0.1016-0.20450.1361-0.26610.16850.0241-0.01640.1279-0.00480.13796.1869-17.2432-0.5097
31.18060.2811-0.64811.6419-0.06925.7619-0.1743-0.0783-0.06190.37240.12690.14270.3516-0.15390.11550.1392-0.0159-0.03450.1628-0.00410.16450.3164-18.73836.7052
41.2697-0.0512-0.71753.56882.30275.84090.0215-0.1186-0.00290.08320.10390.0436-0.34370.1922-0.09590.2101-0.0097-0.00330.1273-0.01190.17215.628-12.47454.9739
55.3003-1.0891.12583.1292-0.41766.03360.0741-0.110.19280.1064-0.0660.1364-0.3674-0.36040.00110.30620.09970.00920.24690.03030.1624-6.7804-9.3223-14.9825
65.17591.08341.05943.34291.02835.6534-0.06320.1451-0.0425-0.34220.1284-0.0541-0.23880.1173-0.08830.22470.01330.00550.15430.01860.09523.5112-15.2744-9.636
78.72744.1686-6.46924.8842-4.11055.2134-0.150.1663-0.1721-0.04180.12760.08360.5018-0.49030.00720.2874-0.0415-0.01870.20510.01030.1814-5.9542-26.97785.0061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 27 )A9 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 71 )A28 - 71
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 95 )A72 - 95
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 154 )A96 - 154
5X-RAY DIFFRACTION5chain 'A' and (resid 155 through 206 )A155 - 206
6X-RAY DIFFRACTION6chain 'A' and (resid 207 through 233 )A207 - 233
7X-RAY DIFFRACTION7chain 'A' and (resid 234 through 254 )A234 - 254

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