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- PDB-8ikd: Structure of DNA binding domain of McrBC endonuclease bound to DN... -

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Basic information

Entry
Database: PDB / ID: 8ikd
TitleStructure of DNA binding domain of McrBC endonuclease bound to DNA: Y41F-L68Y double mutant
Components
  • DNA (5'-D(*GP*AP*GP*AP*CP*CP*GP*GP*TP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*AP*CP*CP*GP*GP*TP*CP*TP*C)-3')
  • Type IV methyl-directed restriction enzyme EcoKMcrB subunit
KeywordsDNA BINDING PROTEIN / McrB-NTD / 5-methylcytosine / restriction endonuclease
Function / homology
Function and homology information


restriction endodeoxyribonuclease activity / endonuclease complex / double-stranded methylated DNA binding / hemi-methylated DNA-binding / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / DNA catabolic process / DNA restriction-modification system / endonuclease activity / GTPase activity / GTP binding ...restriction endodeoxyribonuclease activity / endonuclease complex / double-stranded methylated DNA binding / hemi-methylated DNA-binding / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / DNA catabolic process / DNA restriction-modification system / endonuclease activity / GTPase activity / GTP binding / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding
Similarity search - Function
Type IV methyl-directed restriction enzyme EcoKMcrB subunit, DNA-binding domain / MrcB-like, N-terminal domain / : / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / Type IV methyl-directed restriction enzyme EcoKMcrB subunit
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAdhav, V.A. / Saikrishnan, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis of target recognition by the DNA binding domain of McrBC
Authors: Adhav, V.A. / Saikrishnan, K.
History
DepositionFeb 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type IV methyl-directed restriction enzyme EcoKMcrB subunit
B: Type IV methyl-directed restriction enzyme EcoKMcrB subunit
C: DNA (5'-D(*GP*AP*GP*AP*CP*CP*GP*GP*TP*AP*GP*C)-3')
D: DNA (5'-D(*GP*CP*TP*AP*CP*CP*GP*GP*TP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7516
Polymers47,3324
Non-polymers4182
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-7 kcal/mol
Surface area17060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.909, 68.410, 144.849
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Type IV methyl-directed restriction enzyme EcoKMcrB subunit / EcoKMcrBC / 5-methylcytosine-specific restriction enzyme B


Mass: 19693.938 Da / Num. of mol.: 2 / Mutation: Y41F,L68Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mcrB, rglB, b4346, JW5871 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P15005, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: DNA chain DNA (5'-D(*GP*AP*GP*AP*CP*CP*GP*GP*TP*AP*GP*C)-3')


Mass: 4016.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#3: DNA chain DNA (5'-D(*GP*CP*TP*AP*CP*CP*GP*GP*TP*CP*TP*C)-3')


Mass: 3927.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.88 Å3/Da / Density % sol: 34.55 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1-0.2 M Bis-Tris pH 5.5 and 12-24% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.1→61.86 Å / Num. obs: 20321 / % possible obs: 94.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 32.05 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1594 / CC1/2: 0.603 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SSE

3sse


Resolution: 2.1→39.45 Å / SU ML: 0.2893 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2208
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2479 1978 9.77 %
Rwork0.1988 18259 -
obs0.2037 20237 93.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.55 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 486 28 202 3224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00233727
X-RAY DIFFRACTIONf_angle_d0.47555253
X-RAY DIFFRACTIONf_chiral_restr0.0359548
X-RAY DIFFRACTIONf_plane_restr0.0018506
X-RAY DIFFRACTIONf_dihedral_angle_d22.4239827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.38151210.31691255X-RAY DIFFRACTION91.19
2.15-2.210.36611420.28541267X-RAY DIFFRACTION93.06
2.21-2.280.3841250.32181243X-RAY DIFFRACTION89.82
2.28-2.350.28961440.25821262X-RAY DIFFRACTION93.61
2.35-2.430.29331380.24251259X-RAY DIFFRACTION91.79
2.43-2.530.28911400.23951283X-RAY DIFFRACTION92.76
2.53-2.650.28921330.23531267X-RAY DIFFRACTION92.53
2.65-2.790.29081390.23171271X-RAY DIFFRACTION90.85
2.79-2.960.25031370.20991265X-RAY DIFFRACTION92.18
2.96-3.190.26481340.20711279X-RAY DIFFRACTION91.46
3.19-3.510.25821500.18421332X-RAY DIFFRACTION95.67
3.51-4.020.20371510.1631396X-RAY DIFFRACTION97.54
4.02-5.060.19171400.13891419X-RAY DIFFRACTION98.86
5.06-39.450.19731840.17831461X-RAY DIFFRACTION97.05
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)
16.853741533621.89485149728-1.045205118456.14042297181-0.07454084608066.79029498430.04126879824260.1827450322440.494231153581-0.01650737012620.113893524138-0.569101714697-0.1218579892580.796591706709-0.1522434665530.1994676941580.0148789207114-0.02497976263160.2847046253290.02610376526350.2670289614536.704982331946.97022609232-17.6194703589
25.5233169857-4.208197710490.1423054131746.216019641640.4639843111282.692806753310.01452308827250.2124669615270.0699161400544-0.0047275324305-0.329637311962-0.109092962972-0.3530782857930.1264195866840.2725505600480.254803733172-0.009743431617450.01184497713980.328730006114-0.03388756638260.254212960277-3.2372296533611.2411708067-25.3218713596
33.72142560075-0.7658928292540.3981904149554.95068924145-1.211734853763.766608305610.1243067687880.812164042472-0.323310810193-0.647444685161-0.196321906617-0.06792221139040.443238395830.0772290899580.0139591680640.305567280243-0.05644825453990.01976602430930.391754710496-0.09281439166480.268550325403-8.31143844936-1.36313997204-29.4362262752
40.7397344221280.363618484517-0.2848007229021.96027632256-0.03707852766521.81219647718-0.182897140938-0.0734749604169-0.419305396619-0.1257860371850.2909595789630.04278369979860.514682325125-0.1868038182480.07088593919650.528966247245-0.253007448330.01844677500390.5607926679710.2073085650020.603780374383-3.9943626522-2.022897645223.16918880918
50.2562522032330.226094504622-0.4102217601491.027502500380.4942589474222.96905234593-0.2074434787810.0384854809654-0.132247909249-0.08082008287470.127317889476-0.0635962421440.536632277109-0.0377151327220.1953107928730.3746872280040.214593117753-0.06359257840670.371848266401-0.2348276840190.109070331281-3.98296678591-1.955401864113.18329337975
62.082566639520.54134947651-0.1481478424022.51169297131-0.8216818833134.83861830497-0.02817600347760.2010773984440.04244702037290.0332968169134-0.00830391428774-0.185311717103-0.1735905781530.4707007183580.006766040480940.157546944265-0.0312065878799-0.01637536674440.249078082897-0.0002160187064670.2169893558958.533249791333.8164799256623.2854578591
72.468700856320.221895997141-0.6462324301912.188130227141.79830079441.75446660054-0.151843055711-0.253865610099-0.1529979923490.2080985016230.164391571366-0.01929580706480.3858445975060.1926044949890.02904791704790.2754596157470.0348333595959-0.0119409604840.3116172992850.03401936310290.316845145567.19922132122-9.1189835919924.5824526852
81.555735890080.602515284442-0.357917909391.41422580521-0.2718893182582.44283939335-0.0613240475741-0.013778120212-0.06104736103160.08504760252960.0634228936918-0.1755608079270.06701760258260.115728281750.006338402141450.2227538771590.02657383878520.003302629312230.1841048154620.011622509150.181745549924-2.74417735321-2.1318230772321.7566886215
93.02334144608-0.796723606308-0.9211025399793.84768902956-0.444157046995.782234698-0.0603923511438-0.0865378649029-0.730796705650.3099607643840.1729840194560.05618211258720.733852183144-0.311728753599-0.1412863539510.377046352217-0.148946796442-0.0588267371690.2814042851670.03468067354470.427446341216-11.4043815961-12.750659109126.1002743396
104.68562416168-1.28437313098-2.078966293172.52324523380.6413572892615.489516190030.189256053657-0.2569722086460.205314433537-0.1190510473180.1026987808470.112438209513-0.188614798336-0.298343780006-0.2647125485230.17877547808-0.0195127936935-0.02136075798750.1950780047670.01355676339810.189967433324-14.87560633231.9229157974625.3779346531
114.309579295853.775023420790.2957757323285.07103553681-0.4855115967111.059126408760.0808780195702-0.2554084329310.1385127598360.4660047162230.0468199650335-0.158075615759-0.00106136416545-0.0708385216629-0.107973432750.230272284510.0236346535204-0.03167073203080.242817367633-0.02648601609860.305299964049-4.92191207214.5382957054533.5794728832
122.23592247318-0.1700375047-0.4436079002462.26561182684-0.6092598711081.72633549367-0.0222640919538-0.151238674002-0.282341240390.353252026825-0.04831068249760.06755018082890.403880268195-0.07921426770670.1024375982050.2524085949940.0143033023253-0.0181056436390.2825659159320.01103597167890.292783489144-0.699936143194-11.91012958232.4493646722
133.868612465931.225123477151.718130114111.49997716816-0.2942319423042.28094364971-0.03694665934070.4915472076240.326839936003-0.231860121383-0.02513447992350.387827990139-0.244704982594-0.4068058076170.07168080804110.2672709812070.102428314945-0.005010138967730.4436276718120.05390192801780.418184165549-16.51421527068.73942384205-19.3033255897
144.890831938340.2902489868063.345327696374.610620954794.029598433059.200582843810.147122794047-0.269751103082-0.0512576080460.1044981853470.09266459044960.02689335171420.191375970814-0.593134208872-0.230614085550.2235180313460.002482072405910.05125158404690.3626382254310.02329255579750.265696089344-17.47724554496.11831984059-9.16921102545
151.57689991169-0.169758725452-0.2983197019422.262746786992.15840326953.972767777090.1222680844140.00507003748685-0.0571769740376-0.246005870554-0.0212992068068-0.08082872433320.0828552001313-0.285539364773-0.0789966418210.303145718128-0.0303752778248-0.001331382108880.330332752134-0.02472603706560.320319082151-15.2136670712-4.14827681291-19.4677504018
161.51015697083-0.18020705048-0.1480795901230.745673623555-0.102085938582.464217823950.0154040369083-0.0535061057137-0.144152236648-0.043485872689-0.0165100438845-0.00605114598131-0.166491354834-0.02201470090820.03269482674770.2147830492790.00433626147373-0.01102501055550.1632884080430.01136112306310.1648739264-6.149242040031.43210433156-13.609434202
172.60151008342-1.772683978240.8235501128041.26988297927-0.1644603064013.67428865211-0.04118095705730.0111512277903-0.0154147133886-0.142503665133-0.150755692993-0.3670130264030.00915205173056-0.01597831747480.1615102637420.192546097725-0.01482513364350.04448191205110.283549727395-0.03705903017010.17719883611-1.96730243915.01049830009-21.5162632154
181.66365144272-1.030655290271.979976058522.04242232676-0.9458304253822.435046359640.3413406216930.0197709968808-0.428463776854-0.09993996610020.0404728435548-0.4814779026390.9285730631840.49706696194-0.2837680108290.4031098772230.0569382451858-0.00340434123310.3451024988780.07666958887970.4225024397531.55637132613-9.62469953933-15.718908841
193.063602886131.80870549005-0.5696670059191.16057593195-0.9339377187553.95705295098-0.06793095757880.603671776878-0.339083148199-0.7203763966210.0117391257066-0.0796891770684-0.0917672074647-0.1736857253990.07551461245470.3975709899040.1016426860750.04704762155460.369526410363-0.09103773192780.3759782159476.10780085119-2.86295250309-29.2662158197
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 102 through 120 )BB102 - 120101 - 119
22chain 'B' and (resid 121 through 133 )BB121 - 133120 - 132
33chain 'B' and (resid 134 through 151 )BB134 - 151133 - 150
44chain 'C' and (resid 2 through 13 )CC2 - 13
55chain 'D' and (resid 2 through 13 )DD2 - 13
66chain 'A' and (resid 2 through 27 )AA2 - 271 - 26
77chain 'A' and (resid 28 through 38 )AA28 - 3827 - 37
88chain 'A' and (resid 39 through 82 )AA39 - 8238 - 81
99chain 'A' and (resid 83 through 101 )AA83 - 10182 - 100
1010chain 'A' and (resid 102 through 120 )AA102 - 120101 - 119
1111chain 'A' and (resid 121 through 133 )AA121 - 133120 - 132
1212chain 'A' and (resid 134 through 160 )AA134 - 160133 - 159
1313chain 'B' and (resid 1 through 17 )BB1 - 171 - 17
1414chain 'B' and (resid 18 through 27 )BB18 - 2718 - 27
1515chain 'B' and (resid 28 through 38 )BB28 - 3828 - 38
1616chain 'B' and (resid 39 through 73 )BB39 - 7339 - 73
1717chain 'B' and (resid 74 through 82 )BB74 - 8274 - 82
1818chain 'B' and (resid 83 through 92 )BB83 - 9283 - 92
1919chain 'B' and (resid 93 through 101 )BB93 - 10193 - 100

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