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- PDB-4xpu: The crystal structure of EndoV from E.coli -

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Basic information

Entry
Database: PDB / ID: 4xpu
TitleThe crystal structure of EndoV from E.coli
ComponentsEndonuclease V
KeywordsHYDROLASE / endonuclease V / inosine / DNA repair / RNA cleavage
Function / homology
Function and homology information


deoxyribonuclease V / deoxyribonuclease V activity / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / single-stranded RNA binding / DNA repair / magnesium ion 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 speciesEscherichia coli O45:K1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXie, W. / Zhang, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Sciences Foundation of China31100579 China
Guangdong Innovative Research Team Program2011Y038 China
CitationJournal: Sci Rep / Year: 2015
Title: Crystal structure of E. coli endonuclease V, an essential enzyme for deamination repair
Authors: Zhang, Z. / Jia, Q. / Zhou, C. / Xie, W.
History
DepositionJan 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Data collection
Revision 1.2Nov 8, 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_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease V
B: Endonuclease V


Theoretical massNumber of molelcules
Total (without water)47,8352
Polymers47,8352
Non-polymers00
Water1,982110
1
A: Endonuclease V


Theoretical massNumber of molelcules
Total (without water)23,9181
Polymers23,9181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endonuclease V


Theoretical massNumber of molelcules
Total (without water)23,9181
Polymers23,9181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.892, 84.783, 91.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 4 / Auth seq-ID: 1 - 208 / Label seq-ID: 4 - 211

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.577404, -0.477791, -0.662058), (-0.780248, -0.0841, -0.61979), (0.240451, 0.874439, -0.421355)74.63783, 114.93846, -88.11996

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Components

#1: Protein Endonuclease V / Deoxyinosine 3'endonuclease / Deoxyribonuclease V / DNase V


Mass: 23917.693 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O45:K1 (strain S88 / ExPEC) (bacteria)
Strain: S88 / ExPEC / Gene: nfi, ECS88_4459 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MIY4, deoxyribonuclease V
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 26% PEG 3350, 0.05M sodium fluoride, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 180 K / Ambient temp details: native
Diffraction sourceSource: ROTATING ANODE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jun 1, 2014 / Details: Onyx
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→62.2 Å / Num. obs: 17499 / % possible obs: 99.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 9.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
CrysalisProdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NSP

4nsp


Resolution: 2.4→62.19 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.883 / SU B: 9.83 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.49 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25512 887 5.1 %RANDOM
Rwork0.19484 16581 --
obs0.19791 16581 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.212 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---0.42 Å20 Å2
3---0.95 Å2
Refinement stepCycle: 1 / Resolution: 2.4→62.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 0 110 3352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193322
X-RAY DIFFRACTIONr_bond_other_d0.0170.023245
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9784512
X-RAY DIFFRACTIONr_angle_other_deg0.89537466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3935416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.42722.388134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.20315554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.031530
X-RAY DIFFRACTIONr_chiral_restr0.0840.2500
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02736
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6262.5771670
X-RAY DIFFRACTIONr_mcbond_other1.6242.5761669
X-RAY DIFFRACTIONr_mcangle_it2.6633.8592084
X-RAY DIFFRACTIONr_mcangle_other2.6623.8612085
X-RAY DIFFRACTIONr_scbond_it1.9482.8241652
X-RAY DIFFRACTIONr_scbond_other1.9482.8241652
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2424.1282429
X-RAY DIFFRACTIONr_long_range_B_refined5.4920.7393726
X-RAY DIFFRACTIONr_long_range_B_other5.43420.7183710
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3229 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.480.5
Bmedium thermal3.672
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 66 -
Rwork0.271 1201 -
obs--99.84 %

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