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- PDB-2gb7: Metal-depleted Ecl18kI in complex with uncleaved, modified DNA -

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Basic information

Entry
Database: PDB / ID: 2gb7
TitleMetal-depleted Ecl18kI in complex with uncleaved, modified 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: 1.7 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
DepositionMar 10, 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: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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
Water10,845602
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)77.697, 96.739, 192.012
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 / 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.: 602 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Description: Data for refinement were collected at 1.05 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
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONMPG/DESY, HAMBURG BW611.05, 0.900, 0.9198, 0.9200
SYNCHROTRONMPG/DESY, HAMBURG BW620.9792, 0.9795
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDNov 6, 2002Double focusing X-ray optics
MARRESEARCH2CCDSep 18, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.051
20.91
30.91981
40.921
50.97921
60.97951
ReflectionResolution: 1.7→40 Å / Num. all: 158490 / Num. obs: 158490 / % possible obs: 97.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 31
Reflection shellResolution: 1.7→1.72 Å / Redundancy: 3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.9 / Num. unique all: 5907 / Rsym value: 0.34 / % possible all: 92.6

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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: 1.7→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.763 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: TLS refinement used. The identity of nucleotide 0 (zero) in chains F and H is uncertain (currently assigned as T). See the details in the primary citation.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 7898 10 %RANDOM
Rwork0.207 ---
all0.208 157798 --
obs0.208 157798 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.98 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9695 726 0 602 11023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02210697
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4752.0514585
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0951165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58924.328506
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.312151843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7861570
X-RAY DIFFRACTIONr_chiral_restr0.0950.21600
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027827
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.25643
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.27596
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2705
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.297
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.181.56004
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46329548
X-RAY DIFFRACTIONr_scbond_it2.59135585
X-RAY DIFFRACTIONr_scangle_it3.44.55037
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.73 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 499 -
Rwork0.25 9078 -
obs-10104 92.5 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.06011.19371.25720.92380.72231.52490.3297-0.2254-0.62110.1206-0.0072-0.02570.5275-0.1507-0.32260.2357-0.0738-0.2076-0.21540.11460.474239.19819.7423.922
21.11920.00780.72321.4427-0.32561.49550.1706-0.1297-0.23640.1215-0.0473-0.05510.1070.0675-0.12330.1101-0.0086-0.04110.01070.01510.29455.56638.51230.121
30.8903-0.49040.30312.5858-0.18240.63510.14640.0381-0.253-0.1659-0.01930.10710.1881-0.1445-0.12710.1682-0.0255-0.1108-0.027-0.01060.310625.46532.044.296
41.35440.13250.83930.5682-0.16391.0227-0.01850.04020.0266-0.04220.00920.0164-0.0615-0.03610.00940.11190.0083-0.00140.0098-0.00650.243532.39856.6119.54
50.5822-0.53980.36422.1603-0.1440.4039-0.0339-0.04670.17790.0069-0.0782-0.2669-0.09860.16960.11210.0912-0.0475-0.0220.05570.00710.316578.83483.65829.07
61.7571-0.27030.07330.73570.01880.29480.04760.0092-0.1408-0.0043-0.0379-0.02940.03880.0299-0.00970.10790.0011-0.0130.03630.00890.234670.61459.30927.154
72.19930.38120.91260.49350.20790.8086-0.0883-0.04840.51520.11440.00260.0426-0.1472-0.01020.08580.13810.0005-0.0246-0.0426-0.06510.379255.39996.4931.504
81.17130.2667-0.07130.78810.19930.5540.0481-0.02520.1050.0573-0.08190.09680.0115-0.08120.03390.108-0.0220.00980.0419-0.01570.256739.68877.42723.078
92.12410.49031.35360.8372-0.38933.63270.2683-0.0887-0.3564-0.00970.0163-0.03890.1978-0.1688-0.28470.1604-0.0036-0.0873-0.08080.00560.319339.18432.81416.103
101.4575-0.2230.88062.9092-1.30751.7820.2167-0.0143-0.2446-0.0228-0.00630.12650.1322-0.0708-0.21040.15-0.0405-0.0748-0.02410.01170.304634.17835.47916.409
111.9397-0.4181-0.48392.96610.84451.1109-0.0038-0.03980.07750.10250.0056-0.13050.0292-0.021-0.00180.1128-0.0199-0.00330.058-0.0230.24056480.47830.116
123.1270.3379-0.47921.58150.32411.0215-0.1094-0.10280.2558-0.05170.07930.10640.0560.08210.03010.1294-0.0065-0.00680.0236-0.02340.251960.86583.14226.273
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 145
2X-RAY DIFFRACTION2A153 - 302
3X-RAY DIFFRACTION3B3 - 145
4X-RAY DIFFRACTION4B154 - 305
5X-RAY DIFFRACTION5C4 - 145
6X-RAY DIFFRACTION6C154 - 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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