[English] 日本語
Yorodumi
- PDB-2fqz: Metal-depleted Ecl18kI in complex with uncleaved DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fqz
TitleMetal-depleted Ecl18kI in complex with uncleaved DNA
Components
  • DNA STRAND 1DNA
  • DNA STRAND 2DNA
  • R.Ecl18kI
KeywordsHydrolase/DNA / ECL18KI-DNA COMPLEX / TYPE II RESTRICTION ENDONUCLEASE / NUCLEOTIDE FLIPPING / BASE EXTRUSION / Hydrolase-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding
Similarity search - Function
Restriction Endonuclease - #80 / Restriction endonuclease, type II, EcoRII, C-terminal / EcoRII, C-terminal domain superfamily / EcoRII C terminal / Restriction Endonuclease / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / R.Ecl18kI (Restriction endonuclease)
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsBochtler, M. / Szczepanowski, R.H. / Tamulaitis, G. / Grazulis, S. / Czapinska, H. / Manakova, E. / Siksnys, V.
Citation
Journal: Embo J. / Year: 2006
Title: Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease
Authors: Bochtler, M. / Szczepanowski, R.H. / Tamulaitis, G. / Grazulis, S. / Czapinska, H. / Manakova, E. / Siksnys, V.
#1: Journal: FEBS Lett. / Year: 2002
Title: Alternative arrangements of catalytic residues at the active sites of restriction enzymes.
Authors: Tamulaitis, G. / Solonin, A.S. / Siksnys, V.
#2: Journal: FEBS Lett. / Year: 1998
Title: The Ecl18kI restriction-modification system: cloning, expression, properties of the purified enzymes.
Authors: Denjmukhametov, M.M. / Brevnov, M.G. / Zakharova, M.V. / Repyk, A.V. / Solonin, A.S. / Petrauskene, O.V. / Gromova, E.S.
History
DepositionJan 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 300BIOMOLECULE 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 ...BIOMOLECULE 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). UNDER PHYSIOLOGICAL CONDITIONS Ecl18KI ENDONUCLEASE EXISTS PREDOMINANTLY AS A DIMER (CHAINS AB OR CD), HOWEVER THERE IS SOME EVIDENCE THAT AT HIGH CONCENTRATIONS AND IN SOME CONDITIONS DIMERS MAY ASSOCIATE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: DNA STRAND 1
F: DNA STRAND 2
G: DNA STRAND 1
H: DNA STRAND 2
A: R.Ecl18kI
B: R.Ecl18kI
C: R.Ecl18kI
D: R.Ecl18kI


Theoretical massNumber of molelcules
Total (without water)154,7048
Polymers154,7048
Non-polymers00
Water9,998555
1
E: DNA STRAND 1
F: DNA STRAND 2
A: R.Ecl18kI
B: R.Ecl18kI


Theoretical massNumber of molelcules
Total (without water)77,3524
Polymers77,3524
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: DNA STRAND 1
H: DNA STRAND 2
C: R.Ecl18kI
D: R.Ecl18kI


Theoretical massNumber of molelcules
Total (without water)77,3524
Polymers77,3524
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.371, 95.519, 190.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: DNA chain DNA STRAND 1 / DNA


Mass: 2741.800 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA STRAND 2 / DNA


Mass: 2732.786 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein
R.Ecl18kI / Restriction endonuclease


Mass: 35938.785 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: ecl18kIR / Plasmid: pUC129 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: O87963
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.64 %
Description: Data for refinement were collected at 0.8019 A. MAD data were collected on a bromide soaked crystal (1.05, 0.900, 0.9198, 0.9200) and on a crystal of the selenomethionine variant (0.9792, 0.9795)
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.1
Details: 0.4M (NH4)H2PO4, pH 4.1, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
1,2,31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG X1310.8019
SYNCHROTRONMPG/DESY, HAMBURG BW621.05, 0.900, 0.9198, 0.9200
SYNCHROTRONMPG/DESY, HAMBURG BW630.9792, 0.9795
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDMay 27, 2002BENT MIRROR
MARRESEARCH2CCDNov 6, 2002
MARRESEARCH3CCDSep 18, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1TRIANGULAR MONOCHROMATORSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
3MADMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.80191
21.051
30.91
40.91981
50.921
60.97921
70.97951
ReflectionResolution: 2→20 Å / Num. all: 93417 / Num. obs: 93417 / % possible obs: 93.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.034 / Rsym value: 0.034 / Net I/σ(I): 41
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.12 / Num. unique all: 4852 / Rsym value: 0.24 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
GETAXphasing
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.219 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS refinement used
RfactorNum. reflection% reflectionSelection details
Rfree0.26 4608 5.1 %RANDOM
Rwork0.21 ---
all0.22 90885 --
obs0.22 90885 92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2---0.66 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9638 726 0 555 10919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211387
X-RAY DIFFRACTIONr_angle_refined_deg1.3322.12715675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57151159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87724.342486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.494151799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.081564
X-RAY DIFFRACTIONr_chiral_restr0.0870.21731
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028097
X-RAY DIFFRACTIONr_nbd_refined0.2250.26423
X-RAY DIFFRACTIONr_nbtor_refined0.3120.27804
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2925
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.219
X-RAY DIFFRACTIONr_mcbond_it1.0131.55982
X-RAY DIFFRACTIONr_mcangle_it1.22829486
X-RAY DIFFRACTIONr_scbond_it1.99936691
X-RAY DIFFRACTIONr_scangle_it2.7264.56189
LS refinement shellResolution: 2→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 354 -
Rwork0.23 6054 -
obs-6518 96.4 %
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)
13.78911.99621.44792.38791.03141.90870.7926-0.1943-0.8730.3253-0.1843-0.09660.6122-0.2822-0.60820.0581-0.0628-0.4229-0.27650.13370.422639.45719.40523.764
22.20860.43541.53342.43360.32892.36350.4482-0.0854-0.47230.3595-0.0855-0.290.2380.0434-0.3627-0.0581-0.023-0.1069-0.11130.01420.144756.01138.16529.792
31.7136-0.41311.10832.4372-0.35710.98920.40620.2037-0.5608-0.30350.05630.10230.2755-0.0787-0.4624-0.0049-0.0009-0.2041-0.0843-0.06450.21225.37831.8314.05
42.05980.27831.1690.8006-0.21651.6461-0.08490.18780.0981-0.03930.03030.0284-0.15720.06260.0546-0.0918-0.00330.0069-0.04960.00380.029332.41756.7259.053
50.6802-0.68850.43463.10270.10290.5724-0.1228-0.00170.2561-0.1258-0.0039-0.3082-0.15640.25640.1266-0.1267-0.0801-0.0381-0.00410.01660.157679.4882.79829.072
61.9875-0.17230.19550.6253-0.25640.38890.03560.0774-0.12560.0055-0.0337-0.04330.03130.0579-0.002-0.10380.0031-0.0064-0.0329-0.00890.038971.22158.37126.977
72.38870.88251.19510.90270.3241.0753-0.1892-0.00010.51560.19790.04440.0494-0.1994-0.01210.1448-0.05630.0359-0.0898-0.1668-0.05260.216755.77995.87931.494
81.70460.1234-0.45030.58570.0220.7695-0.00880.01120.1731-0.017-0.00120.073-0.0393-0.09670.0101-0.1089-0.0119-0.0006-0.0384-0.00270.065239.58176.80823.174
94.2214-1.00131.98891.59731.52176.41370.2265-0.1308-0.63010.14720.30090.14550.0591-0.0564-0.5274-0.10750.0184-0.0884-0.1970.04990.10336.85833.91716.031
105.78180.41472.77473.2968-1.912.6930.71750.0511-0.6274-0.3212-0.28320.05050.4734-0.1388-0.4342-0.0121-0.0511-0.0936-0.1162-0.06360.160436.94333.94516.068
111.37861.12031.42413.7802-1.23673.4683-0.2098-0.12940.25230.10540.244-0.1135-0.10480.4462-0.0341-0.1192-0.076-0.0362-0.0579-0.02380.080362.93681.09128.086
125.001-1.2404-0.80442.83651.54080.8408-0.05530.13210.3571-0.0021-0.0475-0.04590.0656-0.2810.1029-0.00630.0640.0281-0.03350.00920.066762.85181.03128.132
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 145
2X-RAY DIFFRACTION2A155 - 302
3X-RAY DIFFRACTION3B4 - 145
4X-RAY DIFFRACTION4B155 - 305
5X-RAY DIFFRACTION5C4 - 145
6X-RAY DIFFRACTION6C155 - 304
7X-RAY DIFFRACTION7D4 - 145
8X-RAY DIFFRACTION8D155 - 304
9X-RAY DIFFRACTION9E-4 - 4
10X-RAY DIFFRACTION10F-4 - 4
11X-RAY DIFFRACTION11G-4 - 4
12X-RAY DIFFRACTION12H-4 - 4

+
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