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- PDB-8ik8: Structure of DNA binding domain of McrBC endonuclease bound to DN... -

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Basic information

Entry
Database: PDB / ID: 8ik8
TitleStructure of DNA binding domain of McrBC endonuclease bound to DNA: L68F 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 restriction-modification system / DNA catabolic process / 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 restriction-modification system / DNA catabolic process / 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: 1.8 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
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-5 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.662, 36.123, 142.805
Angle α, β, γ (deg.)90.000, 98.633, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-242-

HOH

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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
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.: 336 / 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: 2.01 Å3/Da / Density % sol: 38.84 %
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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→47.06 Å / Num. obs: 66256 / % possible obs: 99.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 23.95 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.086 / Net I/σ(I): 8
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1994 / CC1/2: 0.71 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SSE
Resolution: 1.8→47.06 Å / SU ML: 0.1777 / Cross valid method: FREE R-VALUE / σ(F): 0.21 / Phase error: 26.0413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.222 3281 4.96 %
Rwork0.1845 62908 -
obs0.1863 66189 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 486 28 336 3343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01523142
X-RAY DIFFRACTIONf_angle_d1.3414358
X-RAY DIFFRACTIONf_chiral_restr0.0804449
X-RAY DIFFRACTIONf_plane_restr0.0108471
X-RAY DIFFRACTIONf_dihedral_angle_d20.0276590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.3211730.29842519X-RAY DIFFRACTION92.99
1.83-1.860.38331750.29532552X-RAY DIFFRACTION92.63
1.86-1.890.3531380.29832690X-RAY DIFFRACTION91.23
1.89-1.920.36671460.2782533X-RAY DIFFRACTION92.76
1.92-1.950.2911330.27242676X-RAY DIFFRACTION95.74
1.95-1.990.31231260.2632788X-RAY DIFFRACTION95.42
1.99-2.030.27151410.23132667X-RAY DIFFRACTION96.46
2.03-2.080.27391560.24872734X-RAY DIFFRACTION95.6
2.08-2.120.25461310.21872723X-RAY DIFFRACTION96.61
2.12-2.180.28471390.2332712X-RAY DIFFRACTION96.68
2.18-2.240.26791610.20322720X-RAY DIFFRACTION98.23
2.24-2.30.30961400.21582838X-RAY DIFFRACTION98.25
2.3-2.380.24331780.19712717X-RAY DIFFRACTION99.04
2.38-2.460.25221540.20362796X-RAY DIFFRACTION98.4
2.46-2.560.22191340.19572829X-RAY DIFFRACTION98.93
2.56-2.680.17671260.20412769X-RAY DIFFRACTION99.28
2.68-2.820.26441200.20092868X-RAY DIFFRACTION99.14
2.82-2.990.25731300.18612850X-RAY DIFFRACTION98.87
2.99-3.220.20271370.17282761X-RAY DIFFRACTION98.77
3.22-3.550.16581400.14882769X-RAY DIFFRACTION98.44
3.55-4.060.18381470.13382791X-RAY DIFFRACTION97.84
4.06-5.120.15461220.13182832X-RAY DIFFRACTION98.66
5.12-47.060.17351340.16852774X-RAY DIFFRACTION98.81
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)
12.928632445610.334179957609-0.02032712730131.033765385711.343455537215.096136603860.04242516060210.2628430086590.142870684749-0.1484637675770.0582737544850.419568550320.1182849028830.4456057009880.1470946025261.26873611039-0.0284204774463-0.09475483292780.411083211708-0.0919365330918-0.04903380301571.37934585233-10.98894269265.60102591483
25.525538571490.4153099877051.345084511060.1255734383990.5191393029781.948323644360.2962489837230.750782182342-0.421902595664-1.10294647113-0.0376151582126-0.3362530405030.4025958207710.389700597096-0.1976574364080.8531780454140.046582029367-4.04549209868E-50.333463390618-0.02613562579340.25162587936411.3240377768-7.6827789140236.8438754884
35.006656336450.346147627844-0.05582500687345.981713509433.90342006736.37660110986-0.1775905833750.0320009322633-0.1598445470490.0117013558340.22202477209-0.674933847803-0.369396748861.09242725862-0.1025091828690.62016086625-0.0448162915582-0.07105594418750.3451056029420.02637609985360.24921322267610.6530594066-3.8321221654435.3660104809
45.344562412.040810661430.9070699622678.41990368430.9664926203298.439552618540.0828367166656-0.459352201472-0.1306894553730.265834367125-0.163551284502-0.0819286777516-0.614458655369-0.2108178460460.05515348170340.2104617423940.02595730788510.02874905420450.1496961894080.01871522298390.18049278332111.32162572587.3111344550361.1012879893
55.802765647550.9739582628295.098024933832.212723152942.367377204497.84760105906-0.4949326334390.009232388060510.429727951555-0.4297684862290.07448831987190.704679402779-0.899173016876-0.3996918723730.4149636889340.4539876345070.0258880263079-0.02150882228430.238527424320.01769352589490.2518019351648.292682183177.6064928891450.8362360071
61.296351640610.2241741001620.5808312442442.012536698970.9223122432451.71345429933-0.05448970979980.1822311859730.259472765648-0.319751787627-0.052123429348-0.262203395718-0.1311175841830.4315838714480.06073608391280.208597871999-0.01612218335880.04278762690160.2318274547820.05118038586440.18720605901618.71265333461.1727560174651.9406425473
76.524341754371.25565007575-0.7241858669633.92480790899-0.002605561334263.14462800527-0.0580305853814-0.03730471736860.0808373673168-0.2146824956910.05431017539220.006999038244860.0933550659797-0.0128722048454-0.0003851834585640.1504008300450.008227477237540.01084641661830.1348325641140.009592963816450.10461236791913.1267819795-6.0189866271157.3096706301
82.06668843353-0.6137578554570.6473538957712.4815881899-0.1153119427981.766630134540.04326710420930.233091912878-0.125540408318-0.471077608586-0.141046956494-0.2997425836220.1902429878150.5039973256470.03396061526580.1974173186120.01581187934120.06902773144570.2834659519280.02507562430630.23553135793721.5582780942-9.0473714311855.1605961857
93.442020561883.737420898410.5197177393565.900416907160.908259529571.73504955035-0.0654401698645-0.3710118076610.02776239142220.0962366550074-0.413712884987-1.62435571771-0.1802966999020.9545305484040.2022191829590.345731737188-0.0187867102573-0.04972662721220.4265142617380.06760550827360.5154290703427.3785470735-14.670937639264.7042774684
104.797739069722.96231989164-1.774864929156.87901347911-3.675917472.49798231836-0.00522984348780.142995218234-0.0581882107133-0.2592737136120.113729861297-0.05931415212140.5524394490070.148604797241-0.06300191776820.296063980410.00755699989520.02717174573440.122502757429-0.003864370933680.16748710507712.4607032536-16.053679700158.7777814539
117.37295088021-2.1203710170.7608014845035.24912988484-0.5836056012942.64839349447-0.225036864062-0.287393724032-0.1268659204150.5812904821820.1529246342720.357668414752-0.201275343735-0.2292016854620.1336270166260.255703998706-0.01987832672610.06067058927380.1861727811830.01836823197490.14715775895811.0680118985-6.0064131187767.0634688462
122.760653191620.355091253927-0.7393611792393.692712709770.159618155364.35955894047-0.07629396285320.1063403026350.3270571511480.005714246062150.109026616828-0.750404932361-0.06132910223330.704383219206-0.05779712243390.25153971708-0.0514040551253-0.02022777638180.3041764328330.03883170298140.33423832839326.5052975960.84009415473864.1080633988
133.188876208451.81392997741.838681556843.024745597513.585836352334.620244059990.1655750153390.419503186035-0.251492432204-0.399271952487-0.01272962412380.5645454499750.373485641052-0.1867214900040.7349860909861.05088579546-0.106735259107-0.197375554870.301910157980.02455894379970.288747459365-5.99103992999-18.236797846618.2941665995
141.89145972741.057596318341.494081499991.584229279720.1482745045592.570859213630.2879729173550.131454588343-0.304780390358-0.33835306856-0.0687517352618-0.2194950535060.6906637364110.340331936025-0.05840230814280.8703857467470.0370280157687-0.09799837396210.262653025768-0.007157700857430.2532986795262.56849164131-15.159687054221.8565372249
155.32712497786-1.14406275010.5249819322842.05046653602-0.4353784584243.78865217879-0.04432780069370.5035271871360.110490553052-0.433502502429-0.00277202100274-0.153905180318-0.3404343771440.4600011258570.03024373544050.771019847364-0.107353612973-0.05662753210540.320672189202-0.009873447199620.1971459657754.44060907869-3.4966074540114.7953817669
161.889446586861.626809834650.2562366620646.49507683974-0.3790859092360.484908746072-0.338297995280.01182098796080.662912281821-0.145608061318-0.1865214033030.756865787323-0.332382434221-0.194103413775-0.5823451242331.10003062375-0.0699672624065-0.1639830294920.1258387344970.02852301939170.364095548799-3.219707146954.4971044116818.5298933181
174.31336950973-0.0144477553376-4.798625874222.87234285414-1.971705694536.77382828328-0.3793850722890.49458058473-0.345125216465-0.361785673301-0.02731440350880.7918266558710.44444891275-0.677216640341-0.6727709521021.09977853976-0.0793298695503-0.230355326020.3895995748370.01643524411090.245446866843-9.14186213478-5.5163014949412.5184115676
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 134 through 152 )BB134 - 152132 - 150
22chain 'C' and (resid 2 through 13 )CC2 - 13
33chain 'D' and (resid 2 through 13 )DD2 - 13
44chain 'A' and (resid 1 through 17 )AA1 - 171 - 17
55chain 'A' and (resid 18 through 27 )AA18 - 2718 - 27
66chain 'A' and (resid 28 through 62 )AA28 - 6228 - 62
77chain 'A' and (resid 63 through 73 )AA63 - 7363 - 73
88chain 'A' and (resid 74 through 92 )AA74 - 9274 - 92
99chain 'A' and (resid 93 through 101 )AA93 - 10193 - 101
1010chain 'A' and (resid 102 through 120 )AA102 - 120102 - 120
1111chain 'A' and (resid 121 through 133 )AA121 - 133121 - 133
1212chain 'A' and (resid 134 through 158 )AA134 - 158134 - 158
1313chain 'B' and (resid 2 through 17 )BB2 - 171 - 16
1414chain 'B' and (resid 18 through 53 )BB18 - 5317 - 52
1515chain 'B' and (resid 54 through 101 )BB54 - 10153 - 99
1616chain 'B' and (resid 102 through 120 )BB102 - 120100 - 118
1717chain 'B' and (resid 121 through 133 )BB121 - 133119 - 131

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