[English] 日本語
Yorodumi
- PDB-6fb5: Crystal Structure of a Tailored I-CreI Homing Endonuclease Protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fb5
TitleCrystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in complex with an altered version of its target DNA (Haemoglobin beta subunit gene) at 5NNN region in the presence of Magnesium
Components
  • (I-CreI monomer ...) x 2
  • DNA (5'-D(*TP*CP*AP*GP*AP*CP*TP*TP*GP*TP*CP*CP*AP*CP*AP*GP*GP*AP*GP*TP*CP*AP*GP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*CP*TP*CP*CP*TP*GP*TP*GP*GP*AP*CP*AP*AP*GP*TP*CP*TP*GP*A)-3')
KeywordsDNA BINDING PROTEIN / Chlamydomonas reinhardtii
Function / homology
Function and homology information


intron homing / chloroplast / endonuclease activity / Hydrolases; Acting on ester bonds / identical protein binding / metal ion binding
Similarity search - Function
LAGLIDADG endonuclease / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / S-1,2-PROPANEDIOL / DNA / DNA (> 10) / DNA endonuclease I-CreI
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: I-CreI monomer A
B: I-CreI monomer B
D: DNA (5'-D(*TP*CP*AP*GP*AP*CP*TP*TP*GP*TP*CP*CP*AP*CP*AP*GP*GP*AP*GP*TP*CP*AP*GP*A)-3')
F: DNA (5'-D(*TP*CP*TP*GP*AP*CP*TP*CP*CP*TP*GP*TP*GP*GP*AP*CP*AP*AP*GP*TP*CP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,08310
Polymers49,8514
Non-polymers2326
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11850 Å2
ΔGint-99 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.290, 68.005, 83.030
Angle α, β, γ (deg.)90.00, 96.55, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
I-CreI monomer ... , 2 types, 2 molecules AB

#1: Protein I-CreI monomer A


Mass: 17528.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: P05725*PLUS
#2: Protein I-CreI monomer B


Mass: 17583.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: P05725*PLUS

-
DNA chain , 2 types, 2 molecules DF

#3: DNA chain DNA (5'-D(*TP*CP*AP*GP*AP*CP*TP*TP*GP*TP*CP*CP*AP*CP*AP*GP*GP*AP*GP*TP*CP*AP*GP*A)-3')


Mass: 7378.781 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*CP*TP*CP*CP*TP*GP*TP*GP*GP*AP*CP*AP*AP*GP*TP*CP*TP*GP*A)-3')


Mass: 7360.752 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 127 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
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 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→41.24 Å / Num. obs: 47710 / % possible obs: 99.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.54

-
Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G9Y

1g9y


Resolution: 2.2→37.733 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.38
RfactorNum. reflection% reflection
Rfree0.2191 3761 7.88 %
Rwork0.1887 --
obs0.1911 47710 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→37.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2477 978 13 121 3589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0213657
X-RAY DIFFRACTIONf_angle_d0.8215183
X-RAY DIFFRACTIONf_dihedral_angle_d20.3991424
X-RAY DIFFRACTIONf_chiral_restr0.043583
X-RAY DIFFRACTIONf_plane_restr0.003475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.22790.348960.27261186X-RAY DIFFRACTION70
2.2279-2.25720.27761320.261591X-RAY DIFFRACTION90
2.2572-2.28810.28991320.26181529X-RAY DIFFRACTION92
2.2881-2.32080.35381390.25671647X-RAY DIFFRACTION97
2.3208-2.35540.30281420.24961664X-RAY DIFFRACTION98
2.3554-2.39220.31971420.23631698X-RAY DIFFRACTION98
2.3922-2.43140.29161380.23551637X-RAY DIFFRACTION97
2.4314-2.47330.27821450.23581654X-RAY DIFFRACTION96
2.4733-2.51830.27381400.23661666X-RAY DIFFRACTION97
2.5183-2.56670.31721360.23181630X-RAY DIFFRACTION96
2.5667-2.61910.26231490.23651653X-RAY DIFFRACTION97
2.6191-2.67610.26621410.22091624X-RAY DIFFRACTION95
2.6761-2.73830.25741350.21951601X-RAY DIFFRACTION95
2.7383-2.80670.2511410.23231640X-RAY DIFFRACTION94
2.8067-2.88260.29151390.22841629X-RAY DIFFRACTION98
2.8826-2.96740.28561430.21651705X-RAY DIFFRACTION98
2.9674-3.06310.25631450.21581676X-RAY DIFFRACTION98
3.0631-3.17260.21141420.20751623X-RAY DIFFRACTION96
3.1726-3.29950.22191410.18421642X-RAY DIFFRACTION97
3.2995-3.44960.20411460.16421662X-RAY DIFFRACTION96
3.4496-3.63130.19881320.16471590X-RAY DIFFRACTION95
3.6313-3.85860.17641470.17011681X-RAY DIFFRACTION98
3.8586-4.15620.19711430.14821676X-RAY DIFFRACTION98
4.1562-4.57380.14521420.1461663X-RAY DIFFRACTION98
4.5738-5.23420.1811460.16011631X-RAY DIFFRACTION95
5.2342-6.58880.16681410.18521667X-RAY DIFFRACTION98
6.5888-37.73810.20141460.15851684X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 2.2803 Å / Origin y: 15.9742 Å / Origin z: 102.4959 Å
111213212223313233
T0.1002 Å2-0.004 Å20.0233 Å2-0.126 Å20.0147 Å2--0.1177 Å2
L1.7205 °2-0.4469 °20.5751 °2-0.8694 °2-0.3636 °2--1.371 °2
S-0.0062 Å °-0.0206 Å °0.1117 Å °0.0528 Å °-0.1346 Å °-0.0242 Å °-0.018 Å °0.1097 Å °0.03 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://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