[English] 日本語
Yorodumi
- PDB-11qf: I-PnoMI with solubilizing mutations -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 11qf
TitleI-PnoMI with solubilizing mutations
Components
  • (DNA (26-MER)) x 2
  • I-PnoMI
KeywordsDNA BINDING PROTEIN / Homing endonuclease / enzyme / DNA / mutation
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesPhaeosphaeria nodorum (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsDoyle, L. / Stoddard, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM148166 United States
CitationJournal: To Be Published
Title: I-PnoMI with solubilizing mutations
Authors: Stoddard, B.
History
DepositionMar 10, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: I-PnoMI
B: I-PnoMI
C: DNA (26-MER)
D: DNA (26-MER)
E: DNA (26-MER)
F: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,05510
Polymers100,8956
Non-polymers1604
Water8,881493
1
A: I-PnoMI
C: DNA (26-MER)
D: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5285
Polymers50,4483
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-86 kcal/mol
Surface area17980 Å2
MethodPISA
2
B: I-PnoMI
E: DNA (26-MER)
F: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5285
Polymers50,4483
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-88 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.945, 168.234, 76.957
Angle α, β, γ (deg.)90.00, 93.65, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-621-

HOH

-
Components

#1: Protein I-PnoMI


Mass: 34473.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaeosphaeria nodorum (fungus) / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (26-MER)


Mass: 8045.218 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 7929.114 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 21% w/v PEG 3000 0.2 M Ammonium citrate tribasic 50 mM Tris pH 7.5

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.87→46.68 Å / Num. obs: 78761 / % possible obs: 98.2 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.029 / Rrim(I) all: 0.077 / Χ2: 0.99 / Net I/σ(I): 14.3
Reflection shellResolution: 1.87→1.91 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4100 / CC1/2: 0.803 / Rpim(I) all: 0.335 / Rrim(I) all: 0.826 / Χ2: 0.76 / % possible all: 90.3

-
Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
PHASER2.8.3phasing
PDB_EXTRACTdata extraction
XDSdata reduction
Aimless0.7.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→46.68 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 2012 2.56 %
Rwork0.1831 --
obs0.1843 78699 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4645 2123 4 493 7265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017129
X-RAY DIFFRACTIONf_angle_d1.13810116
X-RAY DIFFRACTIONf_dihedral_angle_d22.9182839
X-RAY DIFFRACTIONf_chiral_restr0.0651163
X-RAY DIFFRACTIONf_plane_restr0.009917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.31411480.28425034X-RAY DIFFRACTION91
1.92-1.970.29091330.24995493X-RAY DIFFRACTION99
1.97-2.030.26441360.22455545X-RAY DIFFRACTION99
2.03-2.090.28621500.20895429X-RAY DIFFRACTION99
2.09-2.170.24741380.20815496X-RAY DIFFRACTION99
2.17-2.250.29461560.20515507X-RAY DIFFRACTION98
2.25-2.360.27641430.20125541X-RAY DIFFRACTION99
2.36-2.480.23151340.19955557X-RAY DIFFRACTION99
2.48-2.640.24691590.20095457X-RAY DIFFRACTION99
2.64-2.840.22591390.19915521X-RAY DIFFRACTION98
2.84-3.120.26131480.19565540X-RAY DIFFRACTION99
3.12-3.580.20971310.16865450X-RAY DIFFRACTION97
3.58-4.510.18251490.15385587X-RAY DIFFRACTION99
4.51-46.680.21281480.1645530X-RAY DIFFRACTION98

+
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