[English] 日本語
Yorodumi
- PDB-6fb7: Crystal Structure of the I-CreI Homing Endonuclease D75N variant ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fb7
TitleCrystal Structure of the I-CreI Homing Endonuclease D75N variant in complex with its target DNA in the presence of Manganese
Components
  • DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3')
  • DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3')
  • DNA endonuclease I-CreI
KeywordsDNA BINDING PROTEIN / Chlamydomonas reinhardtii
Function / homology
Function and homology information


intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / metal ion binding / identical protein binding
Similarity search - Function
LAGLIDADG endonuclease / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA endonuclease I-CreI
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.689 Å
AuthorsMolina, R. / Prieto, J.
CitationJournal: Sci Rep / Year: 2018
Title: Understanding the indirect DNA read-out specificity of I-CreI Meganuclease.
Authors: Prieto, J. / Redondo, P. / Lopez-Mendez, B. / D'Abramo, M. / Merino, N. / Blanco, F.J. / Duchateau, P. / Montoya, G. / Molina, R.
History
DepositionDec 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA endonuclease I-CreI
B: DNA endonuclease I-CreI
D: DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3')
E: DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3')
F: DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3')
G: DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8439
Polymers49,6786
Non-polymers1653
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12100 Å2
ΔGint-86 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.504, 169.153, 49.015
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein DNA endonuclease I-CreI / 23S rRNA intron protein


Mass: 17515.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: synthetic construct (others)
References: UniProt: P05725, Hydrolases; Acting on ester bonds
#2: DNA chain DNA (5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3')


Mass: 4248.793 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3')


Mass: 3075.026 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.98 Å3/Da / Density % sol: 58.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M calcium acetate, 0.1 M sodium acetate pH 4.6-5.4, 33-40% (v/v) 1,2-propanediol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.6 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 2.689→49.02 Å / Num. obs: 30910 / % possible obs: 97.1 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.1
Reflection shellResolution: 2.69→2.83 Å

-
Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G9Z

1g9z


Resolution: 2.689→49.015 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.86 / Phase error: 22.21
RfactorNum. reflection% reflection
Rfree0.2114 3097 10.02 %
Rwork0.163 --
obs0.1677 30910 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.689→49.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 980 3 22 3477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093630
X-RAY DIFFRACTIONf_angle_d0.9925121
X-RAY DIFFRACTIONf_dihedral_angle_d21.2621418
X-RAY DIFFRACTIONf_chiral_restr0.053580
X-RAY DIFFRACTIONf_plane_restr0.004476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6889-2.73090.40071100.3243993X-RAY DIFFRACTION75
2.7309-2.77560.34651460.26151289X-RAY DIFFRACTION100
2.7756-2.82350.33611420.2481294X-RAY DIFFRACTION99
2.8235-2.87480.29611500.22611335X-RAY DIFFRACTION100
2.8748-2.93010.29121340.20571265X-RAY DIFFRACTION100
2.9301-2.98990.24611520.22111325X-RAY DIFFRACTION100
2.9899-3.05490.24511440.21731312X-RAY DIFFRACTION100
3.0549-3.1260.25251480.21471267X-RAY DIFFRACTION100
3.126-3.20410.28841480.18471324X-RAY DIFFRACTION100
3.2041-3.29080.21841490.1681296X-RAY DIFFRACTION100
3.2908-3.38760.23161450.1521276X-RAY DIFFRACTION100
3.3876-3.49690.21761510.15661337X-RAY DIFFRACTION100
3.4969-3.62180.20551400.16941287X-RAY DIFFRACTION100
3.6218-3.76680.2295820.1664776X-RAY DIFFRACTION58
3.7668-3.93820.18341370.1511293X-RAY DIFFRACTION100
3.9382-4.14570.18731500.14411308X-RAY DIFFRACTION100
4.1457-4.40530.19911410.12641308X-RAY DIFFRACTION100
4.4053-4.74510.13311440.12661305X-RAY DIFFRACTION100
4.7451-5.22220.19671420.13031302X-RAY DIFFRACTION100
5.2222-5.97670.17621480.14091310X-RAY DIFFRACTION100
5.9767-7.52560.21421430.14841292X-RAY DIFFRACTION100
7.5256-49.02310.15431510.15151319X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 9.4782 Å / Origin y: 192.7005 Å / Origin z: 12.5499 Å
111213212223313233
T0.2928 Å20.0828 Å20.0615 Å2-0.3267 Å20.0443 Å2--0.2415 Å2
L1.8625 °2-1.3057 °21.0541 °2-1.9562 °2-0.9718 °2--2.0652 °2
S-0.2495 Å °-0.1801 Å °-0.1225 Å °0.2191 Å °0.2541 Å °0.1785 Å °-0.0469 Å °0.03 Å °0.0136 Å °
Refinement TLS groupSelection details: all

+
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