[English] 日本語
Yorodumi
- PDB-4xpu: The crystal structure of EndoV from E.coli -

+
Open data


ID or keywords:

Loading...

-
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more