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- PDB-2fqz: Metal-depleted Ecl18kI in complex with uncleaved DNA -

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Basic information

Entry
Database: PDB / ID: 2fqz
TitleMetal-depleted Ecl18kI in complex with uncleaved DNA
Components
  • DNA STRAND 1
  • DNA STRAND 2
  • 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

#1: DNA chain DNA STRAND 1


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


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


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

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Experimental details

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Experiment

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

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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

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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

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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

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