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- PDB-8b4k: Rfa1-N-terminal domain in complex with phosphorylated Ddc2 -

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Basic information

Entry
Database: PDB / ID: 8b4k
TitleRfa1-N-terminal domain in complex with phosphorylated Ddc2
ComponentsReplication factor A protein 1
KeywordsPROTEIN BINDING / Complex / OB-fold / Replication Protein A / DNA damage response / Replication
Function / homology
Function and homology information


heteroduplex formation / sporulation / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / Removal of the Flap Intermediate / telomere maintenance via telomere lengthening / mitotic recombination / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI ...heteroduplex formation / sporulation / DNA replication factor A complex / Gap-filling DNA repair synthesis and ligation in GG-NER / Removal of the Flap Intermediate / telomere maintenance via telomere lengthening / mitotic recombination / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Activation of the pre-replicative complex / Translesion Synthesis by POLH / Termination of translesion DNA synthesis / Activation of ATR in response to replication stress / single-stranded telomeric DNA binding / telomere maintenance via recombination / reciprocal meiotic recombination / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA topological change / Dual incision in TC-NER / telomere maintenance via telomerase / telomere maintenance / condensed nuclear chromosome / meiotic cell cycle / nucleotide-excision repair / establishment of protein localization / double-strand break repair via homologous recombination / single-stranded DNA binding / double-stranded DNA binding / sequence-specific DNA binding / damaged DNA binding / chromosome, telomeric region / DNA replication / protein ubiquitination / DNA repair / mRNA binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Replication factor A protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsYates, L.A. / Zhang, X.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust210658/Z/18/Z United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: A DNA damage-induced phosphorylation circuit enhances Mec1 ATR Ddc2 ATRIP recruitment to Replication Protein A.
Authors: Yates, L.A. / Tannous, E.A. / Morgan, R.M. / Burgers, P.M. / Zhang, X.
History
DepositionSep 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replication factor A protein 1
B: Replication factor A protein 1
C: Replication factor A protein 1


Theoretical massNumber of molelcules
Total (without water)45,7533
Polymers45,7533
Non-polymers00
Water3,855214
1
A: Replication factor A protein 1


Theoretical massNumber of molelcules
Total (without water)15,2511
Polymers15,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Replication factor A protein 1


Theoretical massNumber of molelcules
Total (without water)15,2511
Polymers15,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Replication factor A protein 1


Theoretical massNumber of molelcules
Total (without water)15,2511
Polymers15,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.506, 34.600, 99.350
Angle α, β, γ (deg.)90.000, 90.054, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 0 and (name N or name...
d_2ens_1(chain "B" and ((resid 0 and (name N or name...
d_3ens_1(chain "C" and ((resid 0 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYARGA1 - 36
d_12ens_1LYSPHEA38 - 62
d_13ens_1SERLEUA64 - 125
d_21ens_1GLYPHEB1 - 61
d_22ens_1SERLEUB63 - 124
d_31ens_1GLYARGC1 - 36
d_32ens_1LYSPHEC38 - 62
d_33ens_1SERLEUC64 - 125

NCS oper:
IDCodeMatrixVector
1given(-0.49831358466, 0.86658477864, -0.0267281269921), (-0.866944583056, -0.497708127753, 0.0263383651262), (0.00952162026902, 0.0362965700512, 0.999295700856)32.4060809742, -8.62543176669, 33.6762983923
2given(0.447873514849, 0.893964144049, -0.0154085642467), (0.893492064683, -0.448137860713, -0.02905835755), (-0.0328822907528, -0.000752961150969, -0.999458947633)-6.62056702122, -18.1149287133, -65.7620070063

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Components

#1: Protein Replication factor A protein 1 / RF-A protein 1 / DNA-binding protein BUF2 / Replication protein A 69 kDa DNA-binding subunit / ...RF-A protein 1 / DNA-binding protein BUF2 / Replication protein A 69 kDa DNA-binding subunit / Single-stranded DNA-binding protein


Mass: 15251.147 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RFA1, BUF2, RPA1, YAR007C, FUN3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P22336
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2M Lithium chloride, 0.1M Sodium acetate, pH 5.0, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→54.51 Å / Num. obs: 54483 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 19.8
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.292 / Num. unique obs: 5391 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5omb

5omb


Resolution: 1.55→54.51 Å / SU ML: 0.1395 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.5162
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1903 2688 4.95 %
Rwork0.1681 51584 -
obs0.1692 54272 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.58 Å2
Refinement stepCycle: LAST / Resolution: 1.55→54.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2922 0 0 214 3136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01132973
X-RAY DIFFRACTIONf_angle_d1.36074028
X-RAY DIFFRACTIONf_chiral_restr0.0677458
X-RAY DIFFRACTIONf_plane_restr0.0098528
X-RAY DIFFRACTIONf_dihedral_angle_d16.2929408
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.544343638505
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.746661022474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.580.24111590.20112703X-RAY DIFFRACTION98.79
1.58-1.610.23291650.19442588X-RAY DIFFRACTION98.96
1.61-1.640.19211400.1872704X-RAY DIFFRACTION99.09
1.64-1.680.22651360.1832651X-RAY DIFFRACTION99.54
1.68-1.720.23651500.1812690X-RAY DIFFRACTION99.61
1.72-1.760.22631560.17382662X-RAY DIFFRACTION99.16
1.76-1.810.20661260.17022730X-RAY DIFFRACTION99.44
1.81-1.860.21131480.16512644X-RAY DIFFRACTION99.43
1.86-1.920.19021070.16712775X-RAY DIFFRACTION99.72
1.92-1.990.17971560.16092660X-RAY DIFFRACTION99.75
1.99-2.070.20451270.16882717X-RAY DIFFRACTION100
2.07-2.160.19581070.16072780X-RAY DIFFRACTION99.9
2.16-2.280.18681620.16532677X-RAY DIFFRACTION99.89
2.28-2.420.17941440.16492712X-RAY DIFFRACTION100
2.42-2.610.22161210.16752769X-RAY DIFFRACTION99.97
2.61-2.870.18481580.17082732X-RAY DIFFRACTION100
2.87-3.280.20261580.16732726X-RAY DIFFRACTION99.97
3.28-4.130.18171490.15962755X-RAY DIFFRACTION100
4.14-54.510.16551190.1732909X-RAY DIFFRACTION99.7
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)
18.27882949619-5.3027035085.816806368246.27826873088-5.12157616754.921301543140.0558242887789-0.253129890228-0.05132591035970.1819329868680.08644111985970.104788360503-0.125836858312-0.202618273051-0.2727799585160.229941076247-0.007367328218210.01936225262610.177718441683-0.008036661434290.1686515236264.94782662988-5.41057714991-44.0328913269
25.23259321437-1.462916750223.558487663117.15095319890.03039543370438.80284490470.55553124618-0.322026752402-0.4428212261440.0841110113043-0.2149302573250.1467086203720.7810141019340.00312733366103-0.2412524030780.341189838778-0.0480666231822-0.0493024591320.2400305566810.02582660714810.28153417660510.3546814407-17.5665599497-37.6136975106
33.762217996530.4034264473580.7097117481525.14290253326-0.4964251114294.234020198840.004631147292570.1175245452930.225999045953-0.1009041384550.0301776164835-0.336372209474-0.2218569524380.4126879738050.03362377746160.192803511635-0.01112369455770.01720818850010.174794683368-0.009085585294210.17745061658412.6202212349-3.93937832797-49.2585139671
48.62753876709-6.04130707177-5.17643413994.52214909882.323790732789.074283404370.09287765135990.009635371623650.0945916703031-0.0175079125071-0.145793520937-0.2454439040.1827355882310.378320882674-0.1661903187220.164128811167-0.00426388087508-0.0008866537847270.1735975512250.03032702942880.1885102444917.9065644306-7.24903252646-48.7201703423
56.86708731517-3.140895315770.3709877126942.126909941081.070889251719.013088129670.117562258930.2200285637390.118765976472-0.1030004921920.105093646672-0.2489715022820.05576615513970.631375932699-0.2232517570210.2783777759060.04120198704970.02430709764280.303370918956-0.02545962729070.25265339358616.4185801222-12.2352647736-60.8863218398
64.88459839193-2.42971205918-0.1792016205087.525766984931.939702892016.39874772120.21794545230.3191266194030.228859934141-0.46723390191-0.169398165158-0.116412799098-0.1733451951390.199180261284-0.08500250766220.1771587275740.02153837366910.01571718223170.1463784973340.01222934780310.1482230646699.24202023301-5.60923611838-56.956711363
78.742961309834.857038004656.575289953355.880553952363.784325473058.24980202230.220968538282-0.181488855897-0.204202034337-0.0878214786988-0.21303561719-0.660071350913-0.01368870718920.420789718843-0.05919149224220.266002404278-0.00074179162895-0.03430302438180.2904381774020.04280212986480.30073433983121.035911269-12.106463427-40.5492526049
84.18796975482-1.362416555422.255723262963.951964043630.2627081853156.852577124560.2430612895660.179306457958-0.0595230498026-0.061581049869-0.071916758682-0.1433320781120.2489321206390.424959716332-0.1874713551980.153378899749-0.01867340496760.04516484664950.1545894653840.03703529769760.16608777507412.9969324357-10.3099491999-50.8738193488
93.51802890198-0.3635833137873.534222708683.189309549120.400958334657.36398077980.08327812340590.001480321080140.444705241433-0.145986977414-0.196004426957-0.136483154557-0.329449927767-0.2050771105810.2514683682830.228295822952-0.006483831036090.04435092784010.1373418039350.01084634867440.252637366797.822767626613.98844188772-48.8864257891
101.79020202374-1.1127098545-1.222484073388.50581780471-4.860884021696.11599326315-0.133579544198-0.2570401483560.4027979442970.7115692413640.353550930818-0.299556403114-0.8811139438340.1408916927870.05080696817760.370950331483-0.059160476511-0.06802302132060.297063681148-0.03209603464720.27730894212616.8714811068-0.742493603162-34.6921105068
118.59732672525-4.722900720040.177619585343.99067085007-2.197469481263.86835406678-0.522984245138-1.010942337820.1248981033181.434929153660.483845303495-0.00705250728928-0.327380712104-0.360861473444-0.05440302698440.4777353548150.0281980593748-0.01497470423330.402153446999-0.03157578875420.23851040791715.5662090651-6.41181754611-29.4383394924
122.9467922718-0.381210279728-0.8354334451361.40664386435-0.1435794844884.58480419380.0308386909762-0.299503311512-0.1302846679990.0664810537854-0.01634866667490.009333296226050.1094097882030.1350327597010.001236645420570.272261132815-0.0332139462507-0.01351938397390.38033837640.05258742260140.19709059855820.3857654745-16.4307598067-15.2881659659
138.029928057585.10974070292-5.904177797635.47636379324-3.315373595274.42656377092-0.0567720543215-0.434584558554-0.5255129447950.149606313902-0.375039225383-0.7621866630030.4168814273860.9975965658980.309819847590.3940660191070.0353532192866-0.0222283615420.5622335506690.05133193887290.30945756968333.0331068415-18.5113431712-15.8642278088
145.0794058569-0.6512558680741.003086755134.04551423854-0.617988775857.87616771630.013667755986-0.89456707511-0.1722796658980.245451779795-0.187498666926-0.3051441552211.144285166610.7963113221010.08675761138770.5390387197130.1054695921460.0380263233830.7684733104850.1410402483870.29951879175922.1150421886-21.95645541891.44027656573
154.4251318233-1.519351308832.184587071475.33082617841-2.397404689914.72314284111-0.143060701932-0.549320823525-0.4547966400910.2944373105590.4010700802760.1436564423310.260556153257-0.320113529054-0.3285718234240.269693197544-0.007514378802790.04207625814270.4051257911930.04908421636170.20741932087-11.1341322378-6.81739129545-23.926488614
161.42338891948-0.9654868609090.2386634821296.51990134229-0.9076753264417.638798604390.271343974892-0.394652211131-0.1281074519550.0608653859878-0.0817538032678-0.2743783762080.0546427537650.344353160823-0.2415331020960.2398025727290.01817854992410.05726724886410.5021066042940.055628036220.188815727956-6.57377236222-5.80525891579-16.7530699817
172.63847294273-0.9651213890310.2094968205728.728292694353.479817414016.719105978270.0161485224458-0.6449270810080.1861591993460.2125954621970.107491171845-0.292907222206-0.3110045523850.462078750807-0.2055435885490.225565637095-0.03358801727720.02015937755710.589666869316-0.02193635362760.205115101814-2.37683868569-0.141749177889-17.3199468297
183.29171163023-1.08419430192-0.4368981348328.12504090914-0.8553751144918.926648110730.258745447797-0.7230155366680.1859187662860.3000321113610.0215462513961-0.170923175861-0.617652203852-0.12638786792-0.04589087006760.4063017881920.03108741219950.01846314919850.826164371271-0.0718572747140.236374063389-9.094295719393.73990339026-5.45553777646
190.527573644669-1.255266576290.6999252044436.44996829231-0.0247232064296.50901120158-0.135653172516-0.724006175243-0.07622174655980.4726800971770.283594982918-0.2054485094740.01485404791040.234441668747-0.1181683545530.3091628906740.06994876564790.02777105893160.6864056230060.04992064685390.247132058371-7.02172488107-5.68917764492-9.29384427249
204.513359999836.41598198971-5.82638379229.09659228983-8.267767795087.799740812060.158856811729-0.3541183073390.2888267465030.267933587083-0.00540835696698-0.0318588942621-0.858610070159-0.0386559795922-0.2281373284820.295514302824-0.0169343940326-0.008065636233240.484240979955-0.05153502965120.206095217208-7.305316213287.33734163803-25.9111517598
212.419100825871.3370438692-2.020844334846.716298293-4.301130472754.85060319492-0.074881396951-0.6561143037-0.03406720804690.2917879782520.1308618616710.116594550337-0.01336625982190.22461481113-0.1112046763680.223894439930.0286394796095-0.007857119473650.585224191148-0.03080075711910.194848674842-9.29046684873-0.254591921084-15.3621818476
220.6477024111850.945444402228-0.9342435791275.21058186862-6.401424377657.96928109915-0.320249032203-0.848465904002-0.615743778076-0.0899902588984-0.344099404446-0.9418533533260.5829802731591.110463419630.4941835203860.3579358789930.1454472683920.0605323499220.789003127940.1070212856670.4774568420540.903744375213-11.5905785439-16.1338724418
239.39900459398-2.679438708163.094634286214.36515092364-3.053890356743.1522522570.0153568781502-0.312147348981-0.0224872186865-0.09697233361280.0759501829323-0.0469399396010.0138168902045-0.0319376106468-0.09743671148570.239592925177-0.02684137267030.0414271913310.309273775663-0.01881580015270.197104847149-1.95161970613-0.828126705887-34.0942116838
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 16 )AA0 - 161 - 17
22chain 'A' and (resid 17 through 23 )AA17 - 2318 - 24
33chain 'A' and (resid 24 through 55 )AA24 - 5525 - 48
44chain 'A' and (resid 56 through 62 )AA56 - 6249 - 55
55chain 'A' and (resid 63 through 71 )AA63 - 7156 - 64
66chain 'A' and (resid 72 through 83 )AA72 - 8365 - 76
77chain 'A' and (resid 84 through 94 )AA84 - 9477 - 87
88chain 'A' and (resid 95 through 107 )AA95 - 10788 - 100
99chain 'A' and (resid 108 through 119 )AA108 - 119101 - 112
1010chain 'A' and (resid 120 through 126 )AA120 - 126113 - 119
1111chain 'A' and (resid 127 through 132 )AA127 - 132120 - 125
1212chain 'B' and (resid 0 through 107 )BB0 - 1071 - 99
1313chain 'B' and (resid 108 through 119 )BB108 - 119100 - 111
1414chain 'B' and (resid 120 through 132 )BB120 - 132112 - 124
1515chain 'C' and (resid 0 through 23 )CC0 - 231 - 24
1616chain 'C' and (resid 24 through 33 )CC24 - 3325 - 34
1717chain 'C' and (resid 34 through 62 )CC34 - 6235 - 55
1818chain 'C' and (resid 63 through 71 )CC63 - 7156 - 64
1919chain 'C' and (resid 72 through 83 )CC72 - 8365 - 76
2020chain 'C' and (resid 84 through 94 )CC84 - 9477 - 87
2121chain 'C' and (resid 95 through 107 )CC95 - 10788 - 100
2222chain 'C' and (resid 108 through 119 )CC108 - 119101 - 112
2323chain 'C' and (resid 120 through 132 )CC120 - 132113 - 125

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