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- PDB-7edb: EcoT38I restriction endonuclease complexed with DNA -

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Basic information

Entry
Database: PDB / ID: 7edb
TitleEcoT38I restriction endonuclease complexed with DNA
Components
  • DNA (5'-D(*GP*GP*CP*AP*GP*AP*GP*CP*TP*CP*AP*CP*G)-3')
  • DNA (5'-D(P*CP*GP*TP*GP*AP*GP*CP*TP*CP*TP*GP*C)-3')
  • EcoT38I restriction endonuclease
KeywordsDNA BINDING PROTEIN / Endonuclease
Function / homologyRestriction endonuclease, type II, SacI / SacI restriction endonuclease / endonuclease activity / TRIETHYLENE GLYCOL / DNA / DNA (> 10) / EcoT38I restriction endonuclease
Function and homology information
Biological speciesEscherichia phage P2 (virus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsKita, K. / Mikami, B.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16380061 Japan
CitationJournal: To Be Published
Title: Structural analysis of EcoT38I restriction endonuclease
Authors: Kita, K. / Mikami, B.
History
DepositionMar 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EcoT38I restriction endonuclease
B: EcoT38I restriction endonuclease
E: DNA (5'-D(*GP*GP*CP*AP*GP*AP*GP*CP*TP*CP*AP*CP*G)-3')
F: DNA (5'-D(P*CP*GP*TP*GP*AP*GP*CP*TP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,46424
Polymers85,8344
Non-polymers1,63020
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14260 Å2
ΔGint-104 kcal/mol
Surface area30060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.291, 156.291, 173.049
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein EcoT38I restriction endonuclease


Mass: 38944.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage P2 (virus) / Gene: ecoT38IR / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q83VS8

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DNA chain , 2 types, 2 molecules EF

#2: DNA chain DNA (5'-D(*GP*GP*CP*AP*GP*AP*GP*CP*TP*CP*AP*CP*G)-3')


Mass: 4001.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(P*CP*GP*TP*GP*AP*GP*CP*TP*CP*TP*GP*C)-3')


Mass: 3943.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 7 types, 339 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 68.91 % / Description: bipyramid
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 28% PEG400 0.2 M Calcium chloride 0.1 M Potassium chloride 0.05 M Tris-HCl

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.39→46.41 Å / Num. obs: 49667 / % possible obs: 99.9 % / Redundancy: 12.15 % / Biso Wilson estimate: 39.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.085 / Net I/σ(I): 26.24
Reflection shellResolution: 2.39→2.54 Å / Redundancy: 12.15 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 6.07 / Num. unique obs: 7888 / CC1/2: 0.973 / Rrim(I) all: 0.595 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7E8R

7e8r


Resolution: 2.39→46.41 Å / SU ML: 0.2409 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.7094
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: TLS
RfactorNum. reflection% reflection
Rfree0.1969 2484 5 %
Rwork0.1618 47174 -
obs0.1636 49658 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.82 Å2
Refinement stepCycle: LAST / Resolution: 2.39→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5429 512 97 319 6357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00746238
X-RAY DIFFRACTIONf_angle_d0.8758579
X-RAY DIFFRACTIONf_chiral_restr0.05041001
X-RAY DIFFRACTIONf_plane_restr0.005998
X-RAY DIFFRACTIONf_dihedral_angle_d21.58372315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.440.30011360.22022585X-RAY DIFFRACTION99.67
2.44-2.490.21551360.1972573X-RAY DIFFRACTION99.96
2.49-2.540.25631350.18722563X-RAY DIFFRACTION99.78
2.54-2.60.24611360.17962580X-RAY DIFFRACTION99.89
2.6-2.670.23511350.19172565X-RAY DIFFRACTION99.93
2.67-2.740.25341360.19572599X-RAY DIFFRACTION99.96
2.74-2.820.20961370.19092584X-RAY DIFFRACTION99.93
2.82-2.910.25931360.19052590X-RAY DIFFRACTION100
2.91-3.010.27081370.18472594X-RAY DIFFRACTION99.96
3.01-3.130.21341370.19212609X-RAY DIFFRACTION100
3.13-3.280.25671370.18182608X-RAY DIFFRACTION100
3.28-3.450.21541370.16872599X-RAY DIFFRACTION100
3.45-3.670.16221380.15262617X-RAY DIFFRACTION100
3.67-3.950.19881390.14752639X-RAY DIFFRACTION100
3.95-4.350.16031390.12752657X-RAY DIFFRACTION100
4.35-4.970.14311400.12572658X-RAY DIFFRACTION100
4.97-6.260.16011430.15032713X-RAY DIFFRACTION100
6.26-46.410.17251500.15672841X-RAY DIFFRACTION98.84
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)
11.9212367114-0.02853101795540.2553137567571.75009356528-0.01037722009192.05005294506-0.05208068948750.1868841605750.212623117671-0.2558139990290.027659250129-0.191701044273-0.169840916180.2317070695180.01168692317810.363605201171-0.05029083261650.07474551504950.272175626766-0.03658270843540.360747695337-44.00068171582.13828794284-34.4822885946
22.314617040351.04797422348-0.1588641229771.42442905010.08436017517230.894615232309-0.260710460050.6110767394950.0355801684642-0.3259285424130.1591316819890.112207423171-0.004057174116010.1400245440090.09182723062840.479988368704-0.0191708928933-0.009748709093160.393590898059-0.06447749877920.320039994357-70.5263314622-16.0754095415-42.3042111271
31.103984705120.4833441458640.2855421941210.670743330254-0.02237658625651.32337342909-0.0298242534972-0.07155854387080.263314551905-0.0629482248209-0.0355424323780.213572866546-0.271023262854-0.1504544577490.07040393429420.3675307556330.0367354814974-0.007448686316120.292994540987-0.07671635342510.394450830775-73.6192771668-11.9854971937-25.761676885
41.714903304160.668658449350.3244303223450.9472164850410.03806106581313.099871034880.0884234693457-0.264698230498-0.3076768578750.0530732777412-0.0597670660325-0.05969710644030.489630127729-0.200899445899-0.008170776478950.407433244237-0.02144872671460.01079086889230.275024941413-0.05464843386280.335476013745-75.4884552821-23.8995080105-23.0729662277
53.063145213290.259414759763-0.1879747391881.60758571709-0.05178841926551.2241116595-0.2899446225870.5790085257650.383218611979-0.3211863132370.232785675526-0.00916338898238-0.1732519422920.1580522385910.07986232383420.510643538004-0.05948128287580.01615028492810.3747308085950.006153448083050.322587082384-68.9625105994-11.5265263153-42.8122603396
61.089669236360.0680286478872-0.1486172842651.011827054860.1614878320712.33228472826-0.0143942183578-0.0573620495369-0.1047388325370.1999966137120.0276680971367-0.07362548953570.2168257759570.143149107688-0.01625531257550.3512304700890.0641708669590.004188123626680.256475822438-0.07092580499450.307609373617-51.1965906466-20.8708698809-3.44900983702
72.7452790592-0.6011358528981.631138782660.121396182039-0.3355210190050.941174968110.0585061958842-0.790607762196-0.01244776119630.158278478045-0.1121856484380.3750625518460.648445769562-0.7572940017250.04468610023920.562771651049-0.2209785920340.007907309949620.8279011927250.05339757055010.368238890462-85.2990229077-26.3979650671-14.9189225794
83.046972893840.00981997828877-0.02656265320193.065140028270.2533884859072.998026537930.2883974123890.265292855711-0.209288694996-0.28738097179-0.2924697472440.3229450129210.49609336858-0.6304268269010.003040856892580.510395928462-0.0854250578991-0.08028741555080.484017269881-0.07880371221940.459489790451-96.6498018537-28.4219727578-37.4914084605
93.327966377291.313406331410.2937987204132.01828006674-0.549177890862.510189596430.0257846867117-0.0504366504383-0.389972532865-0.224166236472-0.1722360850340.1208463792840.640252499409-0.3418515955020.1695206228640.594414105339-0.101257669031-0.04691092176210.394957971536-0.1230773275890.443113257509-89.8417360366-33.5782730197-36.0784885295
101.097873671580.225762566844-0.1549738677830.07256727019840.03032442998610.90701289968-0.0316012748018-0.0964024954040.0858795628558-0.02454441671750.0212965722251-0.229179338253-0.007079031234550.002493599080640.02080979801580.4098537512070.04423933956910.01801784125830.330161106963-0.114016958030.347139804532-53.9648482858-13.3690864376-19.9030444586
110.7576662668320.1591193477940.2462321323770.400196103544-0.03747804398090.69538180957-0.0615199574311-0.02234194952050.0711679653991-0.07419389407020.0111554374970.0369446729524-0.1181703831320.07093678860560.04895104792740.4246967852010.03424165521480.04784724763160.279121853203-0.1036645521570.339759111644-54.0854099904-8.58672482062-20.1962873588
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 163 )AA1 - 1631 - 163
22chain 'A' and (resid 164 through 210 )AA164 - 210164 - 210
33chain 'A' and (resid 211 through 252 )AA211 - 252211 - 252
44chain 'A' and (resid 253 through 315 )AA253 - 315253 - 315
55chain 'A' and (resid 316 through 350 )AA316 - 350316 - 351
66chain 'B' and (resid 1 through 163 )BB1 - 1631 - 166
77chain 'B' and (resid 164 through 192 )BB164 - 192167 - 197
88chain 'B' and (resid 193 through 238 )BB193 - 238198 - 241
99chain 'B' and (resid 239 through 349 )BB239 - 349242 - 352
1010chain 'E' and (resid 1 through 13 )EC1 - 13
1111chain 'F' and (resid 1 through 12 )FD1 - 12

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