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- PDB-7r8i: Crystal structure of Pseudooceanicola lipolyticus Argonaute bound... -

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Basic information

Entry
Database: PDB / ID: 7r8i
TitleCrystal structure of Pseudooceanicola lipolyticus Argonaute bound to 5' OH guide DNA in the presence of Mg2+
Components
  • Argonaute
  • DNA (5'-D(*TP*TP*AP*CP*TP*GP*CP*AP*CP*AP*GP*GP*TP*GP*AP*CP*GP*A)
KeywordsHYDROLASE/DNA / argonaute / Ago / DNA guide / RNA cleavage / HYDROLASE-DNA complex
Function / homologynucleic acid binding / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA / DNA (> 10) / Piwi domain-containing protein
Function and homology information
Biological speciesPseudooceanicola lipolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsShin, Y. / Murakami, K.S.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
CitationJournal: To be published
Title: Crystal structure of Pseudooceanicola lipolyticus Argonaute bound to 5' OH guide DNA in the presence of Mg2+
Authors: Shin, Y. / Murakami, K.S.
History
DepositionJun 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Argonaute
T: DNA (5'-D(*TP*TP*AP*CP*TP*GP*CP*AP*CP*AP*GP*GP*TP*GP*AP*CP*GP*A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6043
Polymers93,5792
Non-polymers241
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-22 kcal/mol
Surface area35780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.019, 200.019, 200.019
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Argonaute


Mass: 88038.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudooceanicola lipolyticus (bacteria)
Gene: CVM52_05730 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2M8J4C7
#2: DNA chain DNA (5'-D(*TP*TP*AP*CP*TP*GP*CP*AP*CP*AP*GP*GP*TP*GP*AP*CP*GP*A)


Mass: 5540.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudooceanicola lipolyticus (bacteria)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.56 Å3/Da / Density % sol: 65.48 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris-HCl pH 8.0, 8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 52049 / % possible obs: 100 % / Redundancy: 9.2 % / Biso Wilson estimate: 68.4 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.034 / Χ2: 1.581 / Net I/σ(I): 30
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 1.46 / Num. unique obs: 2601 / CC1/2: 0.472 / Rpim(I) all: 0.691 / Χ2: 1.154 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→44.73 Å / SU ML: 0.407 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.798
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2481 1988 3.82 %
Rwork0.2132 50056 -
obs0.2145 52044 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.63 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6054 347 1 63 6465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00936578
X-RAY DIFFRACTIONf_angle_d1.08938970
X-RAY DIFFRACTIONf_chiral_restr0.0654979
X-RAY DIFFRACTIONf_plane_restr0.01161116
X-RAY DIFFRACTIONf_dihedral_angle_d19.49852503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.41881400.39933557X-RAY DIFFRACTION100
2.46-2.520.38751390.3593533X-RAY DIFFRACTION100
2.52-2.60.37931430.32943544X-RAY DIFFRACTION100
2.6-2.680.3461390.29133547X-RAY DIFFRACTION100
2.68-2.780.33321470.2923592X-RAY DIFFRACTION99.97
2.78-2.890.2761390.2723545X-RAY DIFFRACTION99.97
2.89-3.020.31450.29793539X-RAY DIFFRACTION100
3.02-3.180.30171410.27733553X-RAY DIFFRACTION100
3.18-3.380.27841430.24773585X-RAY DIFFRACTION99.95
3.38-3.640.27721450.21183551X-RAY DIFFRACTION99.97
3.64-4.010.28941360.21493592X-RAY DIFFRACTION100
4.01-4.580.19941400.16753589X-RAY DIFFRACTION100
4.59-5.770.20421430.18283625X-RAY DIFFRACTION100
5.78-44.730.19561480.17273704X-RAY DIFFRACTION99.87
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)
12.731719534280.543556867973-0.1926456632773.231079828690.6685027254442.79799364389-0.1603107150890.0612957124422-0.4024801350550.03695253303290.106528783486-0.789316788310.4582964946510.6204277296120.07101568484480.556097215038-0.03253672186220.04212735560550.6496939763670.1635444299470.754183192734-2.4945734359131.369450522267.4170804256
22.596873427591.879610676070.4704174065824.134555747790.5210748118632.07356060436-0.2510258311240.569087187166-0.190619897999-0.8325223198710.240975338692-0.2932063136830.02467458023760.1003388445560.2667724028760.695898183428-0.1697824414160.07385684657330.76537598782-0.00703767511770.615193179873-17.46350248331.373464118357.5854071746
31.051963451920.4564489307570.307496072181.659994759450.1844305404161.847172940330.137588808784-0.2705721838190.1330074377240.358114074206-0.2171185114190.174748992096-0.439786994645-0.01717934197880.1986763467650.474098197724-0.00487571289204-0.05394323786110.6298082125730.002903507370490.689927827332-5.1440094667.302427227162.9762965522
44.696277504040.3286673133762.571897447023.00158616775-0.03909796884844.531921146240.1979620315190.461432409786-0.355159632347-0.351844556823-0.159888195602-0.118221676054-0.04728957746480.486408064243-0.07905449061740.4152158811990.0123030992279-0.08757085610210.4413563900940.03532556270640.494242853881-4.038907131166.200275900536.7214276575
54.230381289430.850903910999-1.36894023352.58616314289-0.3027063676063.02611637602-0.156188345695-0.243258519472-0.510045269568-0.0400043058507-0.144320557785-0.3751827230190.2551862105420.3556530461460.2516385936870.502372814935-0.032019494263-0.02402070112340.4684190609430.1291895349510.5689932871478.4638880498959.228880728263.5762388494
65.85099516331-4.367686451980.6751426156154.02538030906-1.86338592232.492641072060.2757531437040.739816008525-0.580428470176-1.552680283810.8563381588921.80755924514-0.258839711457-2.310298869430.08790149337711.14487000735-0.226812927263-0.1852614433871.312812580610.2883656511731.07933064011-10.231413611164.052579366550.4169699061
75.81949280646-4.427364789972.667466509093.53249380577-1.669259049466.7197003513-0.1908840052821.08206770137-0.62889672814-0.812296331999-0.05198276158970.7864841312450.6544444648850.184005715438-0.4192628124170.703282097296-0.08350494723490.04533953460020.8235264918510.08029439378441.04681295666-9.6840308738153.969510843961.6130513838
83.09348697416-2.340981033890.8814959524025.43738516549-1.465862263041.22760737375-0.2152684531730.142766297703-0.2413556462840.423198385405-0.146726174219-1.92174788328-0.3310554649380.5185239263620.2551145951830.951703219251-0.107288459458-0.1089026541771.069099711540.1830970773761.23297096274-4.5109779141330.89951950565.376797006
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 242 )AA1 - 2421 - 242
22chain 'A' and (resid 243 through 299 )AA243 - 299243 - 299
33chain 'A' and (resid 300 through 418 )AA300 - 418300 - 418
44chain 'A' and (resid 419 through 548 )AA419 - 548419 - 548
55chain 'A' and (resid 549 through 771 )AA549 - 771549 - 771
66chain 'T' and (resid 0 through 4 )TB0 - 4
77chain 'T' and (resid 5 through 9 )TB5 - 9
88chain 'T' and (resid 10 through 16 )TB10 - 16

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