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- PDB-6seh: Recognition and processing of branched DNA substrates by Slx1-Slx... -

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Basic information

Entry
Database: PDB / ID: 6seh
TitleRecognition and processing of branched DNA substrates by Slx1-Slx4 nuclease
Components
  • Structure-specific endonuclease subunit SLX1
  • Structure-specific endonuclease subunit SLX4
KeywordsDNA BINDING PROTEIN / Resolvase / Structure-Selective endonuclease / Endonuclease
Function / homology
Function and homology information


Slx1-Slx4 complex / organelle organization / 5'-flap endonuclease activity / DNA recombination / DNA replication / Hydrolases; Acting on ester bonds / DNA repair / regulation of DNA-templated transcription
Similarity search - Function
Structure-specific endonuclease subunit Slx4, ascomycetes / Structure-specific endonuclease subunit Slx1 / Structure-specific endonuclease subunit Slx4 / Slx4 endonuclease / HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / GIY-YIG endonuclease / GIY-YIG catalytic domain / GIY-YIG domain profile. / GIY-YIG endonuclease superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Structure-specific endonuclease subunit SLX4 / Structure-specific endonuclease subunit SLX1
Similarity search - Component
Biological speciesThielavia terrestris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.15 Å
AuthorsGaur, V. / Zajko, W. / Nirwal, S. / Szlachcic, A. / Gapinska, M. / Nowotny, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust098022 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease.
Authors: Gaur, V. / Ziajko, W. / Nirwal, S. / Szlachcic, A. / Gapinska, M. / Nowotny, M.
History
DepositionJul 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.4May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Structure-specific endonuclease subunit SLX1
D: Structure-specific endonuclease subunit SLX4
A: Structure-specific endonuclease subunit SLX1
B: Structure-specific endonuclease subunit SLX4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4178
Polymers95,1554
Non-polymers2624
Water18010
1
C: Structure-specific endonuclease subunit SLX1
D: Structure-specific endonuclease subunit SLX4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7094
Polymers47,5782
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-57 kcal/mol
Surface area16000 Å2
MethodPISA
2
A: Structure-specific endonuclease subunit SLX1
B: Structure-specific endonuclease subunit SLX4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7094
Polymers47,5782
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-24 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.322, 63.410, 103.687
Angle α, β, γ (deg.)90.000, 116.697, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein Structure-specific endonuclease subunit SLX1


Mass: 35744.246 Da / Num. of mol.: 2 / Mutation: E79Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thielavia terrestris (fungus) / Gene: SLX1, THITE_2107775 / Production host: Escherichia coli (E. coli)
References: UniProt: G2QV68, Hydrolases; Acting on ester bonds
#2: Protein Structure-specific endonuclease subunit SLX4


Mass: 11833.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thielavia terrestris (fungus) / Gene: SLX4, TT172_LOCUS87 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3S4CYR8
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES (pH 6.0), 0.2 M calcium chloride dihydrate, and 20% (v/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.2828 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2828 Å / Relative weight: 1
ReflectionResolution: 3.15→29.75 Å / Num. obs: 35689 / % possible obs: 97 % / Redundancy: 3.31 % / CC1/2: 0.994 / Net I/σ(I): 8.75
Reflection shellResolution: 3.15→3.33 Å / Redundancy: 3.04 % / Mean I/σ(I) obs: 1.72 / Num. unique obs: 5772 / CC1/2: 0.772 / % possible all: 90

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
SOLVEphasing
PDB_EXTRACT3.25data extraction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.15→29.74 Å / SU ML: 0.5303 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 30.094
RfactorNum. reflection% reflection
Rfree0.2536 3490 9.99 %
Rwork0.2016 --
obs0.2069 34928 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.15→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5053 0 4 10 5067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00285187
X-RAY DIFFRACTIONf_angle_d0.57747061
X-RAY DIFFRACTIONf_chiral_restr0.0402781
X-RAY DIFFRACTIONf_plane_restr0.0059895
X-RAY DIFFRACTIONf_dihedral_angle_d10.05153054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.190.47251380.47671245X-RAY DIFFRACTION96.71
3.19-3.240.49221440.35321256X-RAY DIFFRACTION99.15
3.24-3.290.40291380.32731252X-RAY DIFFRACTION98.09
3.29-3.340.37141390.29151254X-RAY DIFFRACTION97.21
3.34-3.390.3191380.28471228X-RAY DIFFRACTION99.2
3.39-3.450.34961390.27771259X-RAY DIFFRACTION97.83
3.45-3.510.35051390.28391221X-RAY DIFFRACTION96.39
3.51-3.580.2531390.25821265X-RAY DIFFRACTION98.18
3.58-3.650.38211370.27721255X-RAY DIFFRACTION98.24
3.65-3.730.34351450.221268X-RAY DIFFRACTION98.54
3.73-3.820.25471420.22051270X-RAY DIFFRACTION99.23
3.82-3.920.29361370.19951224X-RAY DIFFRACTION99.49
3.92-4.020.24671470.19831287X-RAY DIFFRACTION99.45
4.02-4.140.24931340.18961271X-RAY DIFFRACTION98.74
4.14-4.270.19681330.18151259X-RAY DIFFRACTION99.15
4.27-4.420.26261390.17171255X-RAY DIFFRACTION99.22
4.42-4.60.19591420.16961291X-RAY DIFFRACTION99.24
4.6-4.810.24381390.15471280X-RAY DIFFRACTION99.79
4.81-5.060.2271370.16461265X-RAY DIFFRACTION99.36
5.06-5.380.20831420.17371267X-RAY DIFFRACTION99.16
5.38-5.790.21631380.17361269X-RAY DIFFRACTION99.29
5.79-6.370.25871410.1961274X-RAY DIFFRACTION99.16
6.37-7.280.19941440.1871257X-RAY DIFFRACTION99.22
7.28-9.120.23841430.18271238X-RAY DIFFRACTION98.01
9.12-29.740.21581360.18511228X-RAY DIFFRACTION95.79
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)
12.00931037932-1.362309690310.3975958065641.955751611070.5043348339191.86271675298-0.01983232825520.0533820875539-0.07557377536330.0667212733818-0.0392102324293-0.0620860271240.1146947612070.197758422792-0.08611260163410.5024775249340.00116668432490.007231767235240.394388319012-0.02397422286530.47967115852639.758419003631.378977348234.0315670807
21.628130144890.4010522653420.3404817244043.2838249779-1.947786043243.44510558235-0.1328818616890.379703143761-0.149972602391-0.08005002349410.188217169427-0.01682162016580.109214470997-0.3607942219140.02196775644040.579087974081-0.0529873475849-0.06883225963620.52472594788-0.03005772644670.60575886197828.840201530534.196179777225.59320953
33.59101391206-0.400360167395-0.4172994120911.935138485620.2585682599834.384833879870.195156580380.7626616008990.223417061141-0.0573439516996-0.1025730889330.362992425028-0.700961133212-0.909714148951-0.01784582485330.5704487354710.1057707292390.0265598940460.6795890014550.02759982877330.68165920323924.866016561557.062004141218.5761427391
40.469385674862-0.6705790629680.7949439827521.00617572111-0.3827631101534.129403192720.01879353045850.5652099316720.118403850531-0.58826890305-0.01193851468990.3212543761870.640631129569-0.1741004440840.001982242665590.489186862365-0.08509922547450.03684039203070.6693619022820.05424197669840.70732163994635.168204620247.383326310915.5865048405
54.58185031727-0.8088905049982.467771165753.074046888160.3143319623041.53416183771-0.122516933209-0.2716058173690.2827840805361.456759942170.1107061651011.79966998643-1.934505078720.1404599655240.04591248338791.09341684699-0.03569894084880.1679435801450.601955234176-0.02271377189210.70552050136832.72009037962.249456097843.8009873486
63.1806653077-1.96307569992-3.236108923098.17532364994.557260714694.740365595580.813992121053-0.7470792082510.243074845281-2.05202598678-0.960652944053-1.01589870669-2.949341585590.83304624428-0.07333784437140.866075351794.88426805996E-60.1606775235620.8901792892760.02110701880640.84516401259338.40264180964.257344668122.2908431784
72.779907728080.324043434723-0.4336713370873.97720456011.307602671982.874337593220.157487725403-0.1529454280780.4705436145950.309641247288-0.0733903661926-0.700379517014-0.9357208628720.320657361242-0.1570185647170.948302649065-0.06267367804520.02836673204090.4595964068740.01719265648090.61694049356340.694798251460.715236073433.73038728
83.66259473179-1.284854181450.1982045793413.860316314680.02596014098674.11887358818-0.217067269784-0.241258245062-0.305640181560.9544531940330.423863942599-0.164783853053-0.1921060832810.459081165801-0.3600598903880.739379566790.0767881622296-0.03297015102570.596827612885-0.1164494942920.64597642850640.40946093257.281387103741.542715673
90.478736985367-0.488468930617-0.1267922374192.010910608370.9681790395510.373475826373-0.359259708416-0.1508686009380.535518295631.19157326810.617514827655-0.747377064927-0.1324624653670.436155600215-0.2261990024030.7876784775510.507308862766-0.2260658385071.56383460143-0.3179662985971.1259337876686.774309979511.502345253226.681782065
100.710986850642-0.126245482254-0.4827079901942.65911755123-0.3556344823130.4359821178220.685208911317-1.65731824243-0.976840346260.806759506042-0.2727875455440.1109765411550.8691291909040.324314274451-0.2298116275930.729466211060.458414832424-0.4193761974462.03514660188-0.3369008995451.1706254629787.83502874512.721924998331.7453743351
111.688676371250.35116786952-0.7457935384281.69147972143-0.106041072482.39304267008-0.184705912561-0.6992349066530.3336205263780.5389086354810.111767442625-0.632390592595-0.1734341168080.8802250686860.1413900596411.285248072230.204192055583-0.39282003361.734856583440.04340050774221.2979193421791.826479605411.807412321131.9121055907
121.207203489170.4467565062550.3896654192931.86328626731-0.3504001070290.2603116725010.377426169776-1.04711346171-2.51623296605-0.4214057037790.4513911900730.02269136587471.944602981431.427307520440.389642492091.14840827210.619880827104-0.1003356784711.509898685170.060124226531.4310933153384.95997803960.29522109869923.605530816
133.172217132680.83918895379-1.804940559313.20386743572-0.1702036446931.56565223243-0.1839749388190.1554492550170.210093951758-0.415171335745-0.144323483302-0.1752142711910.2227499151690.7954182165180.2208901614610.5525300699240.2784273410440.05807674575551.241930489260.1420774234630.73001071773989.13504106518.7789526048312.7757989444
140.731525978131-0.265008895352-0.822203910330.3214463841840.4521508420120.9919281836810.176068367974-0.6485180963630.7542952018410.09298285110380.10833190494-0.3889136007790.2113073311150.706818346907-0.1293126301080.8655631082870.0526965749634-0.1318230397561.14189677631-0.04544559543571.0992488733886.829645741623.304057135723.538438069
152.86733239673-1.12908844739-0.9311266738053.355269375330.1590874546124.02821612931-0.1953589708890.4883960221730.0638466430119-0.08029860334850.0746914138710.246306867303-0.2202972321420.1308706702360.1018353563760.6143046548630.00826300103891-0.03602217397370.706001927885-0.06501579159060.60175707406260.912125322619.59291373410.1945542641
164.270303544851.209799759040.4746289864395.74864214382-0.6454180612034.071785823130.0800638487595-0.389891542925-0.08186121547080.640619269632-0.1519223365520.187122428943-0.2477004118070.5515051269190.1261723818660.5405166583710.00885024086294-0.07456638370120.79357868539-0.05357583345790.56728847892566.058742351219.378949461919.9212721457
171.37698112359-0.6649647064440.6133961776851.28796293533-0.7554012438630.605327404386-0.42921299580.1971519602170.585719548424-0.796841658040.199663951697-0.3305475684331.078235463680.324371413727-0.1315128954151.751513286740.1619569387630.2121225746820.857000682382-0.2109388052171.1468686709962.4529653164-7.062674883097.96429292469
184.71810106608-0.4665232118330.552384960325.110486547610.3018880661321.62566134419-0.8808996594390.185767122797-1.53684970762-0.7945162905171.182294910261.09332687011-0.163044983473-0.641555023666-0.2389983311891.01349176959-0.013392602446-0.137217468111.03997075073-0.09617814429971.278730496253.53508697.2554673338917.9845211827
196.22212892281.14978183755-0.06143006139046.50405008652-1.866654650751.96767674862-0.171491889651-2.01407920553-1.31550079479-0.254309808292-0.0791381660048-0.09503630710930.8790490474960.344568585553-0.1937768883571.206890810770.07116429593780.03521204486530.729336896631-0.07985802011920.7038439807861.78531203443.6997179753516.2247269273
200.544397825962-0.1298890886150.1910909589270.2655675011980.4799146883111.67036008161-0.33501096827-1.00116599072-0.312558733015-0.7506738328950.296080809383-0.8307429404211.13873667298-0.077999078688-0.1592356003480.9804395998950.129136987652-0.09779320449670.9109022125990.1040572830580.95926244241466.7284103764.5139961585720.6379701303
210.9283030561430.146558876660.1108920427890.1248686930570.4646774041631.86959200524-0.998551614521-1.13936073589-1.454038831232.28498718044-0.01465809825921.15828054201-0.101227251437-0.7256220438340.9528078162461.378169470990.2388609075870.2667081516470.8933089969560.3778362832741.9626470309160.6106331869-7.5767377755220.6675643529
221.36121065421-0.860861947257-0.4835494852720.749962437019-0.2250676430372.068193963140.9362039432340.647328713206-1.18336324962-0.2747337636980.638088715731.942847783161.69324748179-0.566385018649-0.9620357884311.35444581833-0.102512917514-0.042118256291.14906092083-0.06658617319141.8717786992153.7802605243-9.8834079536111.9592576086
231.32147394018-0.0338139133265-2.176328324677.80316881541-2.934359328375.130658575860.964434027689-0.0686330144468-0.124146417913-0.2221786127930.05452215405241.199223782330.533888015890.0319485825887-1.142922676071.661869621640.2018988219680.05133533936861.15725178129-0.08997704628321.8685097310758.9395459483-15.998573836811.9842246996
242.80207583237-1.639826581430.3195714378641.68017409339-2.338851106666.356271310060.440470394221-0.134122901601-1.03453979010.7568296291131.142247922930.9418104250170.6334653374930.687743711824-0.9345391385761.172761059890.2876214203580.009265588304710.715160830383-0.09498303346870.98543444614170.462349498-6.8706152073714.6172294556
250.451098169537-0.622754534850.298167562742.6991012066-1.014623692470.635080121527-0.765665263328-0.0173729524889-1.733392533010.8007934717840.02862635395580.3247557625821.775163593150.1139116180850.1452950411111.654128430270.2600536740180.02340959401271.043881315760.1378818730511.5551680559670.822049976-2.8262714077621.9874467664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 4 through 143 )
2X-RAY DIFFRACTION2chain 'C' and (resid 144 through 222 )
3X-RAY DIFFRACTION3chain 'C' and (resid 223 through 285 )
4X-RAY DIFFRACTION4chain 'C' and (resid 286 through 312 )
5X-RAY DIFFRACTION5chain 'D' and (resid 844 through 861 )
6X-RAY DIFFRACTION6chain 'D' and (resid 862 through 872 )
7X-RAY DIFFRACTION7chain 'D' and (resid 873 through 899 )
8X-RAY DIFFRACTION8chain 'D' and (resid 900 through 925 )
9X-RAY DIFFRACTION9chain 'A' and (resid 4 through 25 )
10X-RAY DIFFRACTION10chain 'A' and (resid 26 through 41 )
11X-RAY DIFFRACTION11chain 'A' and (resid 42 through 71 )
12X-RAY DIFFRACTION12chain 'A' and (resid 72 through 115 )
13X-RAY DIFFRACTION13chain 'A' and (resid 116 through 169 )
14X-RAY DIFFRACTION14chain 'A' and (resid 170 through 207 )
15X-RAY DIFFRACTION15chain 'A' and (resid 208 through 285 )
16X-RAY DIFFRACTION16chain 'A' and (resid 286 through 311 )
17X-RAY DIFFRACTION17chain 'B' and (resid 849 through 861 )
18X-RAY DIFFRACTION18chain 'B' and (resid 862 through 872 )
19X-RAY DIFFRACTION19chain 'B' and (resid 873 through 878 )
20X-RAY DIFFRACTION20chain 'B' and (resid 879 through 884 )
21X-RAY DIFFRACTION21chain 'B' and (resid 885 through 893 )
22X-RAY DIFFRACTION22chain 'B' and (resid 894 through 900 )
23X-RAY DIFFRACTION23chain 'B' and (resid 901 through 907 )
24X-RAY DIFFRACTION24chain 'B' and (resid 908 through 918 )
25X-RAY DIFFRACTION25chain 'B' and (resid 919 through 925 )

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