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- PDB-8bns: Crystal structure of Pif1 from Sulfurihydrogenibium sp in complex... -

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Basic information

Entry
Database: PDB / ID: 8bns
TitleCrystal structure of Pif1 from Sulfurihydrogenibium sp in complex with ADP
ComponentsAAA ATPase
KeywordsHYDROLASE / Helicase Thermophile
Function / homology
Function and homology information


telomere maintenance / DNA helicase activity / DNA repair
Similarity search - Function
DNA helicase Pif1-like / PIF1-like helicase / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / AAA ATPase
Similarity search - Component
Biological speciesSulfurihydrogenibium sp. YO3AOP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsRety, S. / Chen, W.F. / Xi, X.G.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
Citation
Journal: Microorganisms / Year: 2023
Title: Structural Studies of Pif1 Helicases from Thermophilic Bacteria.
Authors: Rety, S. / Zhang, Y. / Fu, W. / Wang, S. / Chen, W.F. / Xi, X.G.
#1: Journal: Microorganisms / Year: 2023
Title: Structural Studies of Pif1 Helicases from Thermophilic Bacteria.
Authors: Rety, S. / Zhang, Y. / Fu, W. / Wang, S. / Chen, W.F. / Xi, X.G.
History
DepositionNov 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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: AAA ATPase
B: AAA ATPase
C: AAA ATPase
D: AAA ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,8438
Polymers240,1344
Non-polymers1,7094
Water00
1
A: AAA ATPase
B: AAA ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9214
Polymers120,0672
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: AAA ATPase
D: AAA ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9214
Polymers120,0672
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.138, 129.292, 113.685
Angle α, β, γ (deg.)90.000, 103.400, 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 oper:
IDCodeMatrixVector
1given(0.222701245107, -0.0128234698326, -0.974802397437), (0.0141306486175, -0.999765980808, 0.0163801217332), (-0.974784324965, -0.0174224636546, -0.222467924795)253.002076705, 68.5632781916, 318.012579473
2given(0.999994603374, 0.000433414829193, -0.0032565892488), (-0.000428475490312, 0.999998757155, 0.00151726612042), (0.003257242807, -0.00151586256363, 0.999993546244)-6.30062252747, -64.8280937346, 26.3349422869
3given(0.229648997406, -0.00482319146674, -0.973261565467), (0.00187248580612, -0.999983680551, 0.00539744651318), (-0.973271715292, -0.00306193664728, -0.229636218303)244.531871872, 7.09275535485, 344.316550738

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Components

#1: Protein
AAA ATPase


Mass: 60033.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurihydrogenibium sp. YO3AOP1 (bacteria)
Strain: YO3AOP1 / Gene: SYO3AOP1_0527 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: B2V894
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
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: 3.37 Å3/Da / Density % sol: 63.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Tris-HCl 0.1M PEG 4K 20% PEG 200 5%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 3.24→110.59 Å / Num. obs: 31700 / % possible obs: 91.6 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.096 / Rrim(I) all: 0.179 / Net I/σ(I): 5.2
Reflection shellResolution: 3.24→3.57 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1586 / CC1/2: 0.726 / Rpim(I) all: 0.447 / Rrim(I) all: 0.84 / % possible all: 66.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FTD

5ftd


Resolution: 3.24→110.59 Å / Cross valid method: FREE R-VALUE / σ(F): 97.53 / Phase error: 35.247
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2697 1644 5.19 %
Rwork0.2383 30056 -
obs0.2394 31700 62.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.33 Å2
Refinement stepCycle: LAST / Resolution: 3.24→110.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14208 0 108 0 14316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005414636
X-RAY DIFFRACTIONf_angle_d1.010119744
X-RAY DIFFRACTIONf_chiral_restr0.05392140
X-RAY DIFFRACTIONf_plane_restr0.01222484
X-RAY DIFFRACTIONf_dihedral_angle_d15.8775584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.24-3.350.28140.2934198X-RAY DIFFRACTION4.35
3.35-3.460.3163140.3219572X-RAY DIFFRACTION12.54
3.47-3.60.3413430.2851985X-RAY DIFFRACTION21.39
3.6-3.770.3311960.27521492X-RAY DIFFRACTION32.56
3.77-3.970.34751240.25872210X-RAY DIFFRACTION48.18
3.97-4.210.30061530.24663330X-RAY DIFFRACTION72.09
4.21-4.540.28782180.22833872X-RAY DIFFRACTION83.77
4.54-50.24752240.22664293X-RAY DIFFRACTION93.88
5-5.720.24772320.23994377X-RAY DIFFRACTION94.74
5.72-7.210.31192350.25584388X-RAY DIFFRACTION94.59
7.21-110.590.21662220.22024408X-RAY DIFFRACTION93.51
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)
16.9380030513-0.220481192658-1.449884872975.47761420259-0.9226425000336.095140504810.1264001354310.686326874891-0.736367768542-0.41651882296-0.1300135901140.3335451524590.401339977148-0.7465554426490.008662769016250.468761043268-0.00905842421188-0.00715470463420.796982219-0.06512626855680.603839138992222.63133312-28.5637677154.4130437949
26.66365870174-5.26689983291-1.969863157288.626342486245.837990703895.56449987785-0.04569105474130.4808723958490.873073609534-0.1601630114380.643870935491-0.738004937218-0.291093869127-0.170025682112-0.516299505050.591990430875-0.1070743332350.1063403064250.8932596921790.153992281040.697166378879232.341300456-9.6872370030153.5505439273
36.151142853332.589612170461.683683352684.43655113775-2.484784252036.921024164610.0149432040007-0.312599436790.8943968913430.11550831408-0.1978134247150.517811382598-0.4794443386880.609026140080.1430205809610.5362294610480.1623168564-0.1053150626710.745379315927-0.04327940548520.902070991279235.513982206-17.167012226982.1417420457
4-0.7209327299031.18644409059-1.007314448854.794935612452.159321592445.34336877778-0.267147495982-0.3603866240070.495530025871-0.333933756491-0.3609214836220.50942507234-0.234368797125-0.3176986199120.7351348949560.4307929705660.134505911792-0.2481847561760.827493076535-0.08302124463051.23429742712230.17365107-18.774265248970.7934382882
52.574404109252.590875341060.6718781877728.163734715995.218257425189.91969191188-0.106324769459-0.4065031000220.0700883854864-1.53922501021-0.0843266402706-0.924588847487-2.098045952890.4590724300830.07675180933990.898810729419-0.03952110710070.2237462736241.341697797840.1773356065160.980407029649235.765808142-5.008642532151.3612328574
63.56758423315-0.933472621313-2.575732781633.212480398490.2024970718314.985435489660.1690190033430.442282954930.5271896786230.02412969108790.0498169081711-0.16558444853-0.3615648930620.321469945483-0.1913568761580.364826766445-0.01903718814820.03104628840.9355944685560.198968381330.741242731886271.306916317-29.7369424383112.590222992
77.284093452895.544860737621.920710846147.150511800660.6641042984479.32399990876-0.2418678549380.101291849558-1.11739442330.7562733969140.7798005188040.6028642644450.8643223510530.391123404449-0.526638613280.9527074814180.09998036571810.3895688744090.9119516482330.2927253193521.3552717972273.82797889-42.7279796592112.255737795
84.206464171990.7201891146771.238835225542.73077542781-0.7120946043121.427924552580.2413542019970.345354025121-0.472934970898-0.2646863332530.00855516053383-0.393957649850.916775756325-0.252465463169-0.2541840396591.02911596439-0.02498304928020.0823545764960.8275191247820.05303253920980.607336683708255.476408305-42.9596218002100.489814594
94.84554910839-3.2913799841-0.9435568633029.378494270060.253496149922.956013450310.07096590340720.52548042932-0.839557197110.1944004661320.3243814613860.4959715737870.1047053175220.236061283094-0.4014672952270.526385013594-0.00888736449313-0.1037042267960.846327323891-0.350069161860.70634827564226.94835856339.603248748830.2498035755
102.10457242514-3.449702901851.637499307412.200825938043.858670484666.272592348710.786380180108-1.72540585963-1.561545368652.08669854203-1.229375645481.446753901731.69974348051-1.92890371270.3404191930081.06286872447-0.1251950545140.02253586101641.27321299948-0.1761339544141.28701562007231.68658416130.05014792527.0570886779
116.413617758991.785249511730.7493452734393.68652632026-2.356402691021.61804935228-0.1797207373331.57307583448-0.267057964752-0.3698341369920.09407248486890.1301685516470.486570180866-0.2485475592160.08267838616760.649347242290.01732175073920.04251482942290.955766988423-0.281894064680.537299563982236.36072896742.750918316422.7382100744
120.171675839599-2.026881317021.406782861157.47698884451-6.486973917258.33088816680.697019880675-0.084036709486-0.5909716675370.4746846716560.1654788845820.285466648379-1.231906107041.03679581848-0.9286440834830.833517549669-0.3210524226210.009390053058550.991634309797-0.0175003637881.19438507634241.79247326568.760390658238.9030887333
132.22408694579-0.1729127121521.815628591322.802241152850.9051796861753.97999848559-0.3463042684030.3533984911490.5400220292550.106178332322-0.08967913745360.08959042539870.158352214915-0.3581320320110.4393981314690.466359028843-0.09609326610010.002014202801590.8310963604060.1198977198950.677396413721237.18653141541.329582811152.6618567465
141.31977831177-0.693886489676-0.4514499751568.3326673799-4.285040354436.92332958054-0.233276408393-0.3590430937720.142743086369-1.43442316660.5725990350510.4072784327210.03830947663331.17915427647-0.410581433450.826391675505-0.240130913978-0.2988617095350.66393625454-0.1456136172961.08445339248243.66910291456.734895893941.3118873309
150.775494513208-0.266306915140.5739446860864.359141656114.280280976926.36968804731-0.088887225690.4782660352150.20363866849-0.5992742316720.2909673284550.00662247693526-1.395480712541.58777202994-0.3392396700210.90796800373-0.08724323209940.2370372850371.431501900370.1264228857760.95014501927241.90651765159.611363784324.0319772097
169.00240082990.183622819078-1.080515009875.6625685986-1.295337651155.09496180641-0.42411848693-0.194015075665-0.2760758513940.5760348382830.201711204923-0.412068300081-0.356594794881-0.2340850178220.239554014870.453632464325-0.0252721624232-0.0374639874130.532895655348-0.1188251789020.418450947624273.51194627332.720501757489.3803725503
171.0823577565-0.5564921116670.1760937089693.134501556640.5089697617665.5363340544-0.1082187915170.051095583075-0.01811249777670.1443006784150.145752029205-0.1470623794580.6429490943330.888536610207-0.07500147483090.4219935508780.04010419283190.0813131542930.7443819145940.1242985967040.942743181475280.78854553827.395539405281.8279940628
185.9257041839-1.449726352011.659075643087.50034097999-0.5623398174992.311218274570.2462412486810.257799978678-0.204921220611-0.2512277612650.209580962922-0.3216114227211.030781244580.0939661424663-0.4379652928040.950123783554-0.179393783805-0.06456194031470.9302566111740.0389982482840.346331037864255.36060227723.381600871668.3853947713
195.93503419851-0.7395104662551.649261518442.54569690107-1.186880592663.815355081510.3563249772870.610163992118-0.205278927202-0.301706238316-0.30203785958-0.1464134519720.78539248966-0.441044163255-0.07881150372840.69483273239-0.1817309615220.2064893698060.547730916732-0.05198406404770.627511541857263.94817121124.076624934376.2695982824
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 1 through 140 )CE1 - 1401 - 140
22chain 'C' and (resid 141 through 216 )CE141 - 216141 - 216
33chain 'C' and (resid 217 through 318 )CE217 - 318217 - 318
44chain 'C' and (resid 319 through 408 )CE319 - 408319 - 408
55chain 'C' and (resid 409 through 433 )CE409 - 433409 - 433
66chain 'D' and (resid 1 through 160 )DG1 - 1601 - 160
77chain 'D' and (resid 161 through 192 )DG161 - 192161 - 192
88chain 'D' and (resid 193 through 433 )DG193 - 433193 - 433
99chain 'A' and (resid 1 through 85 )AA1 - 851 - 85
1010chain 'A' and (resid 86 through 109 )AA86 - 10986 - 109
1111chain 'A' and (resid 110 through 192 )AA110 - 192110 - 192
1212chain 'A' and (resid 193 through 229 )AA193 - 229193 - 229
1313chain 'A' and (resid 230 through 358 )AA230 - 358230 - 358
1414chain 'A' and (resid 359 through 408 )AA359 - 408359 - 408
1515chain 'A' and (resid 409 through 433 )AA409 - 433409 - 433
1616chain 'B' and (resid 1 through 85 )BC1 - 851 - 85
1717chain 'B' and (resid 86 through 213 )BC86 - 21386 - 213
1818chain 'B' and (resid 214 through 303 )BC214 - 303214 - 303
1919chain 'B' and (resid 304 through 433 )BC304 - 433304 - 433

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