[English] 日本語
Yorodumi
- PDB-1m0i: Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m0i
TitleCrystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site
Componentsendodeoxyribonuclease I
KeywordsHYDROLASE / Holliday junction resolvase / Homodimer / Domain Swapped / Composite active site
Function / homology
Function and homology information


degradation of host chromosome by virus / deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / crossover junction DNA endonuclease activity / double-stranded DNA endonuclease activity / DNA integration / symbiont-mediated suppression of host gene expression / DNA binding
Similarity search - Function
Bacteriophage T7, Gp3, endodeoxynuclease I / Phage endonuclease I / Restriction Endonuclease - #30 / Restriction Endonuclease / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsHadden, J.M. / Declais, A.C. / Phillips, S.E. / Lilley, D.M.
CitationJournal: Embo J. / Year: 2002
Title: Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I
Authors: Hadden, J.M. / Declais, A.C. / Phillips, S.E. / Lilley, D.M.
History
DepositionJun 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: endodeoxyribonuclease I
B: endodeoxyribonuclease I
C: endodeoxyribonuclease I
D: endodeoxyribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5667
Polymers64,2784
Non-polymers2883
Water95553
1
A: endodeoxyribonuclease I
B: endodeoxyribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3314
Polymers32,1392
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-76 kcal/mol
Surface area14320 Å2
MethodPISA
2
C: endodeoxyribonuclease I
D: endodeoxyribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2353
Polymers32,1392
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-59 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.440, 134.550, 61.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsEndonuclease I is active as a homodimer. There are 2 homodimers in the asymmetric unit. Chains A and B form one homodimer.

-
Components

#1: Protein
endodeoxyribonuclease I / endonuclease


Mass: 16069.490 Da / Num. of mol.: 4 / Fragment: Residues 12-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Gene: Endonuclease I / Plasmid: pET 19B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P00641, deoxyribonuclease IV
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.96 Å3/Da / Density % sol: 68.97 %
Crystal growTemperature: 291 K
Method: vapor diffusion, hanging drop. seeds of e65k mutant used.
pH: 7.2
Details: PEG 4000, Ammonium sulphate, Sodium chloride, Tris HCL, pH 7.2, Vapor diffusion, hanging drop. Seeds of E65K mutant used., temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 27, 2001
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.55→33.13 Å / Num. all: 34014 / Num. obs: 34014 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 49.8 Å2 / Rsym value: 0.063 / Net I/σ(I): 9.5
Reflection shellResolution: 2.55→2.68 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 4893 / Rsym value: 0.305 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M0D

1m0d


Resolution: 2.55→33.13 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1192014.82 / Data cutoff high rms absF: 1192014.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Maximum Likelhood target used as implemented in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1686 5 %RANDOM
Rwork0.222 ---
obs0.222 33984 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.1648 Å2 / ksol: 0.357219 e/Å3
Displacement parametersBiso mean: 46.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.67 Å20 Å20 Å2
2---2.71 Å20 Å2
3----2.96 Å2
Refine analyzeLuzzati coordinate error free: 0.41 Å / Luzzati sigma a free: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.55→33.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4097 0 15 53 4165
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.08
LS refinement shellResolution: 2.55→2.64 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.373 175 5.2 %
Rwork0.321 3175 -
obs-3175 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP

+
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://pdbjlvh1.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