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- PDB-4nsp: Crystal structure of human ENDOV -

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Basic information

Entry
Database: PDB / ID: 4nsp
TitleCrystal structure of human ENDOV
ComponentsEndonuclease V
KeywordsHYDROLASE / RAase H-like motif
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXie, W. / Zhang, Z. / Hao, Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of human endonuclease V as an inosine-specific ribonuclease.
Authors: Zhang, Z. / Hao, Z. / Wang, Z. / Li, Q. / Xie, W.
History
DepositionNov 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endonuclease V


Theoretical massNumber of molelcules
Total (without water)27,9361
Polymers27,9361
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.750, 48.713, 108.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 27936.400 Da / Num. of mol.: 1 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENDOV / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8N8Q3, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.88 Å3/Da / Density % sol: 34.6 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: 0.2M sodium formate, 0.1 M Tris-HCl PH7.5,19%PEG3350, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: Nova high-flux-micro-focus sealed tube / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Sep 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→26.76 Å / Num. all: 9877 / Num. obs: 9828 / % possible obs: 99.5 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2.2 / Redundancy: 3.7 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 9.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1404 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CrysalisProdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
CrysalisProdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HD0

3hd0


Resolution: 2.3→26.755 Å / SU ML: 0.28 / σ(F): 1.5 / σ(I): 2.2 / Phase error: 25.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2683 471 4.8 %4.8%
Rwork0.2097 ---
all0.2126 9877 --
obs-9803 99.32 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27 Å2
Refinement stepCycle: LAST / Resolution: 2.3→26.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 0 84 1932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041881
X-RAY DIFFRACTIONf_angle_d0.8892544
X-RAY DIFFRACTIONf_dihedral_angle_d14.171703
X-RAY DIFFRACTIONf_chiral_restr0.063294
X-RAY DIFFRACTIONf_plane_restr0.003329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.63260.30961540.23463063X-RAY DIFFRACTION100
2.6326-3.31590.30781520.23013107X-RAY DIFFRACTION100
3.3159-26.7570.231650.18743162X-RAY DIFFRACTION98

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