[English] 日本語
Yorodumi
- PDB-9xy1: One of a series of engineered variants of I-OnuI meganuclease tar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9xy1
TitleOne of a series of engineered variants of I-OnuI meganuclease targeting altered DNA target sequence
Components
  • (DNA (26-MER)) x 2
  • eI-OnuI_P456_TGA
KeywordsDNA BINDING PROTEIN / meganuclease / structure prediction / protein engineering / DNA BINDING PROTEIN-DNA complex
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.923 Å
AuthorsWerther, R. / Stoddard, B.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM139752 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM105691 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM148166 United States
CitationJournal: To Be Published
Title: Prediction, modeling and design of protein-DNA recognition via computational and machine learning approaches: accomplishments and remaining challenges
Authors: Esler, M.A. / Werther, R. / Bradley, P. / Stoddard, B.L.
History
DepositionAug 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: eI-OnuI_P456_TGA
B: DNA (26-MER)
C: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,96813
Polymers50,5233
Non-polymers44510
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-139 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.671, 70.440, 165.936
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein eI-OnuI_P456_TGA


Mass: 34551.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

-
DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (26-MER)


Mass: 7974.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 7997.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 153 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM sodium acetate pH 5.0, 200mM calcium acetate, 40% PEG 400

-
Data collection

DiffractionMean temperature: 108 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 35463 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 34.19 Å2 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.017 / Rrim(I) all: 0.061 / Χ2: 0.96 / Net I/σ(I): 10.2 / Num. measured all: 447964
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.92-1.9912.10.66534420.90.1980.6940.876
1.99-2.07130.43935000.9610.1260.4570.895
2.07-2.1612.80.30435070.9780.0880.3170.906
2.16-2.2812.10.21734990.9880.0650.2270.934
2.28-2.4213.20.17235180.9930.0490.1780.96
2.42-2.6112.90.11634980.9970.0330.1211.014
2.61-2.8712.40.08435090.9980.0250.0870.947
2.87-3.2813.10.05535730.9990.0160.0570.983
3.28-4.1412.60.04236000.9990.0120.0441.024
4.14-50120.03838170.9990.0110.041.048

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.24 Å43.5 Å
Translation6.24 Å43.5 Å

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.7.16phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.923→41.484 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 1999 5.65 %
Rwork0.2048 33381 -
obs0.207 35380 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.57 Å2 / Biso mean: 37.3179 Å2 / Biso min: 16.97 Å2
Refinement stepCycle: final / Resolution: 1.923→41.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 1060 28 143 3501
Biso mean--55.47 38.89 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013512
X-RAY DIFFRACTIONf_angle_d1.1264978
X-RAY DIFFRACTIONf_chiral_restr0.061568
X-RAY DIFFRACTIONf_plane_restr0.007453
X-RAY DIFFRACTIONf_dihedral_angle_d21.4481886
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.923-1.97090.34361360.2582226997
1.9709-2.02410.33071420.23642373100
2.0241-2.08370.30921390.22072323100
2.0837-2.15090.27661420.21152368100
2.1509-2.22780.27881400.20672343100
2.2278-2.3170.25151410.20852357100
2.317-2.42250.29071440.21782397100
2.4225-2.55020.26841400.21252338100
2.5502-2.70990.28061420.21692382100
2.7099-2.91910.25171430.22572375100
2.9191-3.21270.2541460.2112433100
3.2127-3.67740.2111420.18712389100
3.6774-4.63210.20851470.18112437100
4.6321-41.4840.22211550.20952597100

+
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