[English] 日本語
Yorodumi
- PDB-3fd2: Crystal structure of mMsoI/DNA complex with calcium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fd2
TitleCrystal structure of mMsoI/DNA complex with calcium
Components
  • 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3'
  • 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3'
  • Site-specific DNA endonuclease I-MsoI
KeywordsHYDROLASE/DNA / Protein-DNA complex / Chloroplast / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


chloroplast / endonuclease activity
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) / Site-specific DNA endonuclease I-MsoI
Similarity search - Component
Biological speciesMonomastix sp. (plant)
Monomastix sp. OKE-1
unidentified (others)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsLi, H. / Monnat, R.J.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins.
Authors: Li, H. / Pellenz, S. / Ulge, U. / Stoddard, B.L. / Monnat, R.J.
History
DepositionNov 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Apr 9, 2014Group: Source and taxonomy
Revision 1.3Jun 28, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_entity_src_syn / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _struct_ref_seq.db_align_beg ..._entity.pdbx_description / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg
Revision 1.4Sep 6, 2023Group: 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Site-specific DNA endonuclease I-MsoI
B: 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3'
C: 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8475
Polymers56,7673
Non-polymers802
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-74 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.932, 41.933, 70.960
Angle α, β, γ (deg.)107.21, 95.43, 109.44
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Site-specific DNA endonuclease I-MsoI


Mass: 42024.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fusion protein comprises residues 1-170 of I-MSOI, a linker of 33 residues (TGSGSGSKHPTLTLPTTTSQENLPNGSGSGSGT) and a 2nd I-MSOI (1-170 residues).
Source: (gene. exp.) Monomastix sp. (strain OKE-1) (plant), (gene. exp.) Monomastix sp. OKE-1, unidentified
Strain: OKE-1
Gene: orf170, the chloroplast large subunit rDNA intron gene
Plasmid: pET system / Production host: Escherichia coli (E. coli) / Strain (production host): C2566
References: UniProt: C0JWR6, Hydrolases; Acting on ester bonds
#2: DNA chain 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3'


Mass: 7419.792 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: the physiological DNA target site of I-MsoI in the chloroplast large subunit rDNA of Monomastix
Source: (synth.) synthetic construct (others)
#3: DNA chain 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3'


Mass: 7321.716 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: the physiological DNA target site of I-MsoI in the chloroplast large subunit rDNA of Monomastix
Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Sequence details33 RESIDUES OF LINKER (TGSGSGSKHPTLTLPTTTSQENLPNGSGSGSGT) INSERTED BETWEEN TWO I-MSOI PROTEINS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.4 %
Crystal growTemperature: 291 K / pH: 7.3
Details: 22% PEG 400, 100 mM Tris pH 7.3, 10 mM calcium chloride, 20 mM sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 11073 / % possible obs: 97 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 21
Reflection shellResolution: 2.69→2.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 4.51 / % possible all: 95.8

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M5X

1m5x


Resolution: 2.69→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.901 / SU ML: 0.422 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.281 546 4.8 %RANDOM
Rwork0.211 ---
obs0.215 10862 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å24.6 Å2-6.76 Å2
2--1.75 Å2-3.57 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.69→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2720 978 2 35 3735
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.11
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.064
X-RAY DIFFRACTIONr_gen_planes_refined0.003
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.198
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.304
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.142
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 37 -
Rwork0.294 749 -
obs--90.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8289-0.04763.13881.616-1.604516.9580.2676-0.0824-0.27250.01340.2930.1840.1332-0.2923-0.5606-0.23-0.02790.0697-0.2531-0.01560.080316.300713.7601-7.5468
24.0403-1.18614.82171.8423-1.733718.44471.1348-0.6091-0.8251-0.37180.58430.53922.7998-2.0788-1.71910.0243-0.5052-0.2767-0.26440.25190.145711.48526.2318-8.4028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 178
2X-RAY DIFFRACTION1A207 - 367
3X-RAY DIFFRACTION2B501 - 524
4X-RAY DIFFRACTION2C551 - 574

+
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