[English] 日本語
Yorodumi
- PDB-5e5o: I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e5o
TitleI-SmaMI bound to uncleaved DNA target in the presence of Calcium ions
Components
  • DNA (25-MER)
  • I-SmaMI LAGLIDADG endonuclease
  • Top strand DNA (25-MER)
KeywordsHYDROLASE/DNA / LAGLIDADG / I-SmaMI / Complex / uncleaved / HYDROLASE-DNA complex
Function / homology
Function and homology information


endonuclease activity / mitochondrion / 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
DNA / DNA (> 10) / Homing endonuclease LAGLIDADG domain-containing protein
Similarity search - Component
Biological speciesSordaria macrospora (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsShen, B.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH R01 GM105691 United States
CitationJournal: J.Mol.Biol. / Year: 2016
Title: The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease.
Authors: Shen, B.W. / Lambert, A. / Walker, B.C. / Stoddard, B.L. / Kaiser, B.K.
History
DepositionOct 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
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-SmaMI LAGLIDADG endonuclease
B: DNA (25-MER)
C: Top strand DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,06713
Polymers49,5133
Non-polymers55510
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-65 kcal/mol
Surface area18310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.327, 67.993, 97.743
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein I-SmaMI LAGLIDADG endonuclease


Mass: 34155.707 Da / Num. of mol.: 1 / Fragment: UNP residues 114-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sordaria macrospora (strain ATCC MYA-333 / DSM 997 / K(L3346) / K-hell) (fungus)
Strain: ATCC MYA-333 / DSM 997 / K(L3346) / K-hell / Gene: SMAC_12671 / Plasmid: pET21d(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)RIL+ / References: UniProt: F7WD42

-
DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (25-MER)


Mass: 7691.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Top strand DNA (25-MER)


Mass: 7664.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 90 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG MME550, HEPES / PH range: 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 70 / Detector: CCD / Date: Sep 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.36→27 Å / Num. obs: 17265 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 14.8
Reflection shellResolution: 2.36→2.44 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 2 / % possible all: 93.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LOX

4lox


Resolution: 2.36→27 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.911 / SU B: 23.483 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.537 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27353 827 4.8 %RANDOM
Rwork0.18789 ---
obs0.19209 16388 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.645 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2---0.07 Å20 Å2
3---1.03 Å2
Refinement stepCycle: 1 / Resolution: 2.36→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 1019 31 80 3476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0173567
X-RAY DIFFRACTIONr_bond_other_d0.0020.022969
X-RAY DIFFRACTIONr_angle_refined_deg2.0861.6945009
X-RAY DIFFRACTIONr_angle_other_deg1.32336896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5065295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.89224.3397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15715455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.04158
X-RAY DIFFRACTIONr_chiral_restr0.1270.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023242
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02789
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
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_it1.5032.2561177
X-RAY DIFFRACTIONr_mcbond_other1.4962.2541176
X-RAY DIFFRACTIONr_mcangle_it2.53.3771470
X-RAY DIFFRACTIONr_mcangle_other2.53.3811471
X-RAY DIFFRACTIONr_scbond_it1.5142.4152390
X-RAY DIFFRACTIONr_scbond_other1.5142.4152390
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4443.5773539
X-RAY DIFFRACTIONr_long_range_B_refined4.0319.7724311
X-RAY DIFFRACTIONr_long_range_B_other4.0319.7764312
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.361→2.422 Å
RfactorNum. reflection% reflection
Rfree0.382 57 5 %
Rwork0.294 1054 -
obs--89.24 %
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)
11.00570.586-0.25512.7478-1.95832.2309-0.0091-0.0255-0.1411-0.0337-0.0158-0.03640.1370.14560.02490.13940.02950.0010.0545-0.00650.0279-5.97040.9794-0.9113
20.1466-0.09850.313.272-3.38124.2828-0.0356-0.1048-0.07290.1209-0.1408-0.1801-0.06450.22140.17640.26840.0264-0.02790.23190.07440.22244.1170.7107-0.9076
30.40280.1596-0.18681.9759-2.91495.24780.007-0.0393-0.00060.0573-0.0817-0.1379-0.14640.26850.07470.28370.06010.01490.17060.05080.16544.001-0.1984-1.2606
44.939-7.49544.849817.2853-11.82348.13310.10150.0168-0.2527-0.0491-0.2039-0.07130.02380.15140.10240.22860.00970.05720.264-0.02080.2364-2.6803-2.3929-2.033
50.320.01540.0410.6985-0.32260.39750.00510.0149-0.0315-0.11890.00650.07350.0939-0.0037-0.01160.21430.0230.00110.1292-0.00010.016-4.52594.7081-4.5516
61.09911.61080.14742.36620.2170.0244-0.05690.0622-0.1223-0.04880.0752-0.175-0.0307-0.0395-0.01820.490.22410.14960.52020.05320.1450.997510.4236-16.6212
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 300
2X-RAY DIFFRACTION2B1 - 25
3X-RAY DIFFRACTION3C1 - 25
4X-RAY DIFFRACTION4A401 - 403
5X-RAY DIFFRACTION5A501 - 545
6X-RAY DIFFRACTION5B201 - 220
7X-RAY DIFFRACTION5C201 - 215
8X-RAY DIFFRACTION6A404 - 405
9X-RAY DIFFRACTION6B101 - 102
10X-RAY DIFFRACTION6C101

+
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