[English] 日本語
Yorodumi
- PDB-5dwc: Crystal structure of restriction endonuclease AgeI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dwc
TitleCrystal structure of restriction endonuclease AgeI
ComponentsType-2 restriction enzyme AgeI
KeywordsHYDROLASE / restriction endonuclease / PD-(D/E)XK nuclease
Function / homologyBsaWI restriction endonuclease type 2 / BsaWI restriction endonuclease type 2 / type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / Type II restriction enzyme AgeI
Function and homology information
Biological speciesThalassobius gelatinovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsTamulaitiene, G. / Ramonaite, I. / Grazulis, S. / Siksnys, V.
Funding supportLithuania, 1items
OrganizationGrant numberCountry
Research Council of LithuaniaMIP-41/2013Lithuania
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA.
Authors: Tamulaitiene, G. / Jovaisaite, V. / Tamulaitis, G. / Songailiene, I. / Manakova, E. / Zaremba, M. / Grazulis, S. / Xu, S.Y. / Siksnys, V.
History
DepositionSep 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2May 3, 2017Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type-2 restriction enzyme AgeI


Theoretical massNumber of molelcules
Total (without water)30,5941
Polymers30,5941
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.213, 59.269, 120.915
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Type-2 restriction enzyme AgeI / R.AgeI / Endonuclease AgeI / Type II restriction enzyme AgeI


Mass: 30593.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thalassobius gelatinovorus (bacteria) / Gene: ageIR / Plasmid: pRRS-AgeIRM / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q9KHV6, type II site-specific deoxyribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystallization buffer was 0.1 M NaCl, 0.1 M Na-Hepes (pH 7.5), 22% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.91 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2014 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.5→33.329 Å / Num. all: 9795 / Num. obs: 9795 / % possible obs: 100 % / Redundancy: 5.8 % / Biso Wilson estimate: 31.5 Å2 / Rpim(I) all: 0.057 / Rrim(I) all: 0.141 / Rsym value: 0.118 / Net I/av σ(I): 5.859 / Net I/σ(I): 12.5 / Num. measured all: 56770
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.645.90.6471.1812613760.3120.6473100
2.64-2.85.90.4541.6786913250.2170.4544.3100
2.8-2.995.90.2972.4730212370.1410.2976.2100
2.99-3.235.90.2183.3687911630.1040.2188.2100
3.23-3.545.80.1255.6636710890.060.12513.1100
3.54-3.955.80.0779.158119990.0370.07718.7100
3.95-4.565.80.0513.850818790.0240.0523.7100
4.56-5.595.70.0513.342727530.0240.0523.1100
5.59-7.915.40.04315.133126080.0220.04321.9100
7.91-33.3294.80.0291717513660.0150.02929.498.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.82 Å33.33 Å
Translation2.82 Å33.33 Å

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
MOSFLM7.0.6data reduction
SCALA3.3.20data scaling
MOLREP6phasing
Coot0.6.1model building
PHENIX1.8.3refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DWB

5dwb


Resolution: 2.5→33.329 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.256 867 9.75 %Random selection
Rwork0.2142 16087 --
obs0.2186 9756 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.25 Å2 / Biso mean: 36.9635 Å2 / Biso min: 4.48 Å2
Refinement stepCycle: final / Resolution: 2.5→33.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 0 19 2145
Biso mean---22.26 -
Num. residues----274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022171
X-RAY DIFFRACTIONf_angle_d0.6762938
X-RAY DIFFRACTIONf_chiral_restr0.026321
X-RAY DIFFRACTIONf_plane_restr0.003388
X-RAY DIFFRACTIONf_dihedral_angle_d13.22807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.57370.33431430.29671315X-RAY DIFFRACTION100
2.5737-2.65680.37151390.27381347X-RAY DIFFRACTION100
2.6568-2.75170.33031380.28351338X-RAY DIFFRACTION100
2.7517-2.86180.34191370.26651365X-RAY DIFFRACTION100
2.8618-2.9920.27881400.26281347X-RAY DIFFRACTION100
2.992-3.14960.3531260.25321356X-RAY DIFFRACTION100
3.1496-3.34670.28821550.23841335X-RAY DIFFRACTION100
3.3467-3.60490.27041360.22291335X-RAY DIFFRACTION100
3.6049-3.96710.21371610.20121339X-RAY DIFFRACTION100
3.9671-4.53990.19641450.16391344X-RAY DIFFRACTION100
4.5399-5.71510.22791410.1651349X-RAY DIFFRACTION100
5.7151-33.3290.19431760.16721317X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.2321 Å / Origin y: 0.3455 Å / Origin z: 15.8391 Å
111213212223313233
T0.1627 Å20.0159 Å20.016 Å2-0.1667 Å2-0.0025 Å2--0.1554 Å2
L0.8943 °20.1175 °2-0.0307 °2-2.0066 °20.7983 °2--0.9572 °2
S0.0688 Å °-0.0211 Å °0.0135 Å °-0.2533 Å °-0.0102 Å °-0.1799 Å °-0.107 Å °-0.0168 Å °0.0077 Å °
Refinement TLS groupSelection details: chain A

+
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