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- PDB-6qzk: Structure of Clostridium butyricum Argonaute bound to a guide DNA... -

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Basic information

Entry
Database: PDB / ID: 6qzk
TitleStructure of Clostridium butyricum Argonaute bound to a guide DNA (5' deoxycytidine) and a 19-mer target DNA
Components
  • Clostridium butyricum Argonaute
  • DNA target (5'-D(T*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*T)-3')
  • siDNA guide (5'-D(P*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')
KeywordsHYDROLASE / Argonaute / pAgo / AGO / CbAgo
Function / homologyFORMIC ACID / DNA / DNA (> 10)
Function and homology information
Biological speciesClostridium butyricum (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.548 Å
AuthorsSwarts, D.C. / Jinek, M. / Hegge, J.W. / Van der Oost, J.
Funding support Switzerland, Netherlands, 6items
OrganizationGrant numberCountry
European Molecular Biology OrganizationALTF 179-2015 Switzerland
European Molecular Biology OrganizationaALTF 509-2017 Switzerland
Swiss National Science FoundationSNSF 31003A_149393 Switzerland
Netherlands Organisation for Scientific Research711013002 Netherlands
Netherlands Organisation for Scientific Research714.015.001 Netherlands
Netherlands Organisation for Scientific Research016.Veni.192.072 Netherlands
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute.
Authors: Hegge, J.W. / Swarts, D.C. / Chandradoss, S.D. / Cui, T.J. / Kneppers, J. / Jinek, M. / Joo, C. / van der Oost, J.
History
DepositionMar 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jun 26, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Clostridium butyricum Argonaute
B: siDNA guide (5'-D(P*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')
C: DNA target (5'-D(T*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3389
Polymers98,0843
Non-polymers2546
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Momomeric CbAgo bound to a siDNA guide and target DNA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint-60 kcal/mol
Surface area38180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.450, 181.450, 142.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Clostridium butyricum Argonaute


Mass: 85827.000 Da / Num. of mol.: 1 / Mutation: D541A, D611A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium butyricum (bacteria) / Plasmid: pML-1M / Production host: Escherichia coli BL21 (bacteria)

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain siDNA guide (5'-D(P*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')


Mass: 6573.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA target (5'-D(T*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*T)-3')


Mass: 5683.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 9 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.46 Å3/Da / Density % sol: 64.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: NaForm, Nickel chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.548→76.606 Å / Num. obs: 17344 / % possible obs: 99.89 % / Redundancy: 39 % / Biso Wilson estimate: 110.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.2808 / Rrim(I) all: 0.2845 / Net I/σ(I): 17.05
Reflection shellResolution: 3.548→3.675 Å / Redundancy: 38 % / Rmerge(I) obs: 1.876 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 1696 / CC1/2: 0.861 / Rrim(I) all: 1.907 / % possible all: 99.94

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GQ9

5gq9


Resolution: 3.548→76.606 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.18
RfactorNum. reflection% reflection
Rfree0.2759 1729 9.98 %
Rwork0.2473 --
obs0.2501 17332 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.548→76.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6033 697 16 3 6749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046946
X-RAY DIFFRACTIONf_angle_d0.729503
X-RAY DIFFRACTIONf_dihedral_angle_d16.7784063
X-RAY DIFFRACTIONf_chiral_restr0.0491052
X-RAY DIFFRACTIONf_plane_restr0.0041083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.548-3.65240.3531400.33161267X-RAY DIFFRACTION100
3.6524-3.77030.3471410.3171270X-RAY DIFFRACTION100
3.7703-3.9050.37691410.31231266X-RAY DIFFRACTION100
3.905-4.06140.31891410.28761272X-RAY DIFFRACTION100
4.0614-4.24620.28891430.27171286X-RAY DIFFRACTION100
4.2462-4.470.26531420.25371279X-RAY DIFFRACTION100
4.47-4.75010.26441420.23721277X-RAY DIFFRACTION100
4.7501-5.11670.23981440.22171301X-RAY DIFFRACTION100
5.1167-5.63150.29811450.24521300X-RAY DIFFRACTION100
5.6315-6.44610.31261450.2641308X-RAY DIFFRACTION100
6.4461-8.11990.26441490.25131338X-RAY DIFFRACTION100
8.1199-76.62410.21441560.19131439X-RAY DIFFRACTION100
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)
11.7647-1.42671.25444.01781.21442.6674-0.20160.0882-0.0781-0.4615-0.0858-1.2441-0.0522-0.0770.12520.8494-0.12410.16880.80770.04361.3008-62.2079-5.8317-14.636
23.95681.3593-0.4725.2460.90811.3205-0.1040.35130.195-0.20890.1998-0.8022-0.19290.2468-0.11180.65160.10450.03040.6969-0.01990.9622-66.9043-19.6609-17.5354
37.42871.71021.73265.8212.02945.4896-0.3092-0.95820.73821.47670.13870.79140.95781.46880.36611.01770.0586-0.20291.3662-0.23911.4272-60.9519-27.2703-0.4555
43.7866-0.2187-1.60691.1251-0.53651.04140.137-0.11320.51690.84940.8527-1.2787-0.34110.7125-0.81831.0554-0.0252-0.20680.7758-0.18891.1153-78.8635-26.3088-1.1147
52.48531.69052.57671.23371.65253.746-0.15611.4059-0.0196-0.471-0.41160.45870.18810.7551.2481.2330.360.00131.5240.07711.1265-84.7183-8.4615-9.6263
62.0111-0.40410.9242.8910.74832.6279-0.72560.16980.30951.21520.02160.2768-0.0145-0.13940.50381.5384-0.0934-0.20170.7827-0.12611.5032-87.1049-14.6922-7.3507
75.2433-1.4163-2.28183.73722.88072.51330.21630.33430.40750.12850.18480.0479-0.61010.2875-0.27281.29720.04-0.09760.77410.02221.0444-66.8648-32.66181.4593
82.1846-1.08070.35942.5958-0.57130.114-0.02860.04830.50890.1902-0.1377-0.5695-0.2349-0.010.2350.8705-0.0611-0.12890.5725-0.1621.0527-100.9735-17.2168-17.4378
93.138-1.7268-0.08733.4673-0.93274.265-0.2518-0.20360.7440.05230.16081.1085-0.0287-0.16330.27520.6676-0.0558-0.05020.536-0.06521.0144-108.0867-16.9239-16.9356
100.8228-0.3720.29971.89650.46771.8651-0.0109-0.11860.19610.5743-0.00320.00120.4273-0.2246-0.17960.8291-0.04050.08940.6243-0.03830.769-94.508-26.5964.2295
111.75520.4177-0.21741.62640.92650.6394-0.12230.0146-0.17960.43510.1209-0.24210.21490.1975-0.09930.88040.0899-0.0880.6050.10310.9193-75.5759-28.4639-2.3066
121.2562-2.02430.13983.7744-0.39790.0881-0.2387-0.04881.21640.50180.4778-2.4705-0.06350.577-0.27351.01090.2486-0.26051.3168-0.40991.7342-43.5839-22.2187.6859
132.1326-1.2080.84772.55380.26473.0623-0.0947-0.422-0.0925-0.07150.4775-0.7511-0.05230.1884-0.20890.7797-0.0543-0.14650.7853-0.14871.6449-52.8467-21.46360.4124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 544 through 617 )
2X-RAY DIFFRACTION2chain 'A' and (resid 618 through 748 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 5 )
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 10 )
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 17 )
6X-RAY DIFFRACTION6chain 'C' and (resid -18 through -9 )
7X-RAY DIFFRACTION7chain 'C' and (resid -8 through -1 )
8X-RAY DIFFRACTION8chain 'A' and (resid 1 through 48 )
9X-RAY DIFFRACTION9chain 'A' and (resid 49 through 108 )
10X-RAY DIFFRACTION10chain 'A' and (resid 109 through 237 )
11X-RAY DIFFRACTION11chain 'A' and (resid 238 through 400 )
12X-RAY DIFFRACTION12chain 'A' and (resid 401 through 449 )
13X-RAY DIFFRACTION13chain 'A' and (resid 450 through 543 )

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