[English] 日本語
Yorodumi
- PDB-4lq0: Crystal structure of the I-LtrWI LAGLIDADG homing endonuclease bo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lq0
TitleCrystal structure of the I-LtrWI LAGLIDADG homing endonuclease bound to target DNA.
Components
  • LAGLIDADG homing endonuclease
  • bottom strand DNA target
  • top strand DNA target
KeywordsHYDROLASE/DNA / LADLIDADG / protein-DNA complex / Homing endonuclease / Hydrolase / HYDROLASE-DNA complex
Function / homology
Function and homology information


endonuclease activity / mitochondrion
Similarity search - Function
LAGLIDADG endonuclease / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / LAGLIDADG homing endonuclease I-LtrII
Similarity search - Component
Biological speciesLeptographium truncatum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsChik, J. / Shen, B. / Stoddard, B.
CitationJournal: To be Published
Title: Structural Comparisons of LAGLIDADG Homing Endonucleases.
Authors: Chik, J. / Shen, B. / Stoddard, B.
History
DepositionJul 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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: LAGLIDADG homing endonuclease
B: top strand DNA target
C: bottom strand DNA target
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4788
Polymers51,1293
Non-polymers3485
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-91 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.553, 71.959, 168.648
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 LAGLIDADG homing endonuclease / LAGLIDADG homing endonuclease I-LtrII


Mass: 35158.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptographium truncatum (fungus) / Strain: win(M)1435 / Gene: small subunit rbosomal RNA, mitochondrial / Plasmid: pET21D / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) RIL+ / References: UniProt: E0YCK3

-
DNA chain , 2 types, 2 molecules BC

#2: DNA chain top strand DNA target


Mass: 8001.189 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain bottom strand DNA target


Mass: 7970.178 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Non-polymers , 4 types, 23 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG MME 550 0.1 M Bis-Tris 50 mM Calcium Chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2012 / Details: mirrors
RadiationMonochromator: single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.68→44.5 Å / Num. all: 14522 / Num. obs: 13839 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 11.3 % / Biso Wilson estimate: 47.67 Å2 / Rsym value: 0.092 / Net I/σ(I): 20
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.68-2.811.34.213380.586195
2.8-2.9111.33.413570.4195

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERMRphasing
REFMAC5.7.0025refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3qqy

3qqy


Resolution: 2.68→44.34 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.894 / SU B: 30.631 / SU ML: 0.278 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27148 688 5 %RANDOM
Rwork0.19683 ---
obs0.20037 13100 94.59 %-
all-13780 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.566 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.33 Å2-0 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.68→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2421 1060 18 18 3517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0173667
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.6945159
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6125297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06625.364110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.49915490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.722157
X-RAY DIFFRACTIONr_chiral_restr0.1180.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022335
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.68→2.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 40 -
Rwork0.288 860 -
obs--85.96 %
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)
11.3175-1.01931.22412.1474-2.05525.24930.08240.0601-0.1595-0.1247-0.05480.01960.1404-0.0101-0.02760.0548-0.0140.02680.0946-0.01340.3015-11.7679-1.925641.296
21.6908-0.6516-0.732.70760.607310.96120.12810.03120.09510.1074-0.0554-0.1985-0.5429-0.0853-0.07270.0454-0.0102-0.00930.12880.0440.1792-6.40015.952344.2324
31.7292-0.3931-1.17732.1053-0.430612.76040.24470.12920.12740.00230.0526-0.1467-0.86340.6523-0.29730.11760.0069-0.0160.14350.03170.1707-5.60845.705642.43
40.01730.11320.0466227.137478.730627.2937-0.08830.0235-0.0658-2.51760.6016-1.3293-0.89360.2236-0.51330.6291-0.02020.02960.4159-0.14230.68552.0019.969423.4737
51.7053-1.8571.7372.1145-2.43885.52590.28340.09950.0581-0.0978-0.1444-0.0631-0.75150.5872-0.1390.3938-0.0956-0.01660.0888-0.04930.105-6.4873.467747.3932
611.043721.7616.490543.561311.07968.28260.1655-0.1045-0.63470.5136-0.062-1.3843-0.6017-0.2145-0.10350.5328-0.01490.01490.4775-0.02510.39-9.014-5.59628.1574
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 304
2X-RAY DIFFRACTION2B1 - 26
3X-RAY DIFFRACTION3C1 - 26
4X-RAY DIFFRACTION4B101
5X-RAY DIFFRACTION5A501 - 512
6X-RAY DIFFRACTION5C201 - 202
7X-RAY DIFFRACTION5B201 - 204
8X-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://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