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- PDB-5g5t: Structure of the Argonaute protein from Methanocaldcoccus janasch... -

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Basic information

Entry
Database: PDB / ID: 5g5t
TitleStructure of the Argonaute protein from Methanocaldcoccus janaschii in complex with guide DNA
Components
  • ARGONAUTE
  • GUIDE DNA
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / ARGONAUTE / BACTERIAL DEFENSE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Site specific endodeoxyribonucleases: cleavage is not sequence specific (deleted sub-subclass) / clearance of foreign intracellular DNA / DNA endonuclease activity / defense response to virus / DNA binding / RNA binding / metal ion binding
Similarity search - Function
: / : / Archaeal argonaute protein N-terminal domain / Argonaute, PAZ domain, archaea / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ domain profile. ...: / : / Archaeal argonaute protein N-terminal domain / Argonaute, PAZ domain, archaea / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ domain profile. / PAZ domain / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesMETHANOCALDOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSchneider, S. / Oellig, C.A. / Keegan, R. / Grohmann, D. / Zander, A. / Willkomm, S.
CitationJournal: Nat Microbiol / Year: 2017
Title: Structural and mechanistic insights into an archaeal DNA-guided Argonaute protein.
Authors: Willkomm, S. / Oellig, C.A. / Zander, A. / Restle, T. / Keegan, R. / Grohmann, D. / Schneider, S.
History
DepositionJun 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARGONAUTE
D: GUIDE DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,99210
Polymers91,2952
Non-polymers6978
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.950, 117.950, 134.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ARGONAUTE


Mass: 84706.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q58717
#2: DNA chain GUIDE DNA


Mass: 6588.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4

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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: 2.66 Å3/Da / Density % sol: 0.43 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.85→44.4 Å / Num. obs: 22659 / % possible obs: 1 % / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 102.61 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.8
Reflection shellResolution: 2.85→3 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.1 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5G5S

5g5s


Resolution: 2.85→49.11 Å / Cor.coef. Fo:Fc: 0.9334 / Cor.coef. Fo:Fc free: 0.8976 / SU R Cruickshank DPI: 1.499 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.592 / SU Rfree Blow DPI: 0.391 / SU Rfree Cruickshank DPI: 0.396
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5407. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5407. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=3. GUIDE DNA NUCLEOTIDES 8 TO 18 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1146 5.06 %RANDOM
Rwork0.2287 ---
obs0.2315 22659 99.41 %-
Displacement parametersBiso mean: 96.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.6747 Å20 Å20 Å2
2---0.6747 Å20 Å2
3---1.3494 Å2
Refine analyzeLuzzati coordinate error obs: 0.573 Å
Refinement stepCycle: LAST / Resolution: 2.85→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5239 138 36 0 5413
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015531HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.287555HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1848SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes129HARMONIC2
X-RAY DIFFRACTIONt_gen_planes774HARMONIC5
X-RAY DIFFRACTIONt_it5531HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion23.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion760SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6104SEMIHARMONIC4
LS refinement shellResolution: 2.85→2.99 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.3201 157 5.3 %
Rwork0.2442 2803 -
all0.2484 2960 -
obs--99.41 %
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)
10-0.87132.08377.0547-3.19412.6324-0.13270.34890.12650.00250.2027-0.391-0.43710.6346-0.07-0.3170.02310.03110.22270.22590.025924.3816-25.2874-4.6191
22.4559-5.8744-1.1110.9562-5.824700.1508-0.260.43140.09270.00680.3362-0.7688-0.0429-0.1577-0.1081-0.1643-0.0197-0.02970.20070.249414.941-3.672-13.8858
31.47570.2748-0.15611.6312-3.26880-0.04430.63830.3806-0.2664-0.4308-0.3875-0.27230.29840.4751-0.2701-0.0784-0.0190.19480.247-0.079418.2849-21.9878-13.8487
42.47081.1011.86932.82720.27753.2182-0.15210.35280.2333-0.3472-0.08380.49490.26130.37040.2359-0.2090.01170.0193-0.12340.069-0.01421.7771-29.1027-20.9183
50-2.5692-0.520503.19183.96220.0914-0.10770.038-0.285-0.2596-0.26270.64120.01110.1682-0.30560.0482-0.11460.27410.25330.10668.8936-40.168822.7823
66.11954.54310.76149.26854.91084.46160.1335-1.1557-0.8754-0.7902-0.94821.02250.0338-0.9060.8147-0.3186-0.0764-0.07090.0347-0.0399-0.2015-18.2695-45.204922.159
77.06735.7269-3.89783.6896-3.52290.2777-0.191-0.44530.3213-1.11220.20040.1440.606-0.5534-0.0094-0.17540.1964-0.2525-0.0395-0.2933-0.1494-19.6818-38.895914.0623
86.0499-0.5577-0.38586.93591.0984.5490.1988-0.09150.8337-0.0162-0.45870.2318-0.837-0.55230.2599-0.28530.1163-0.08920.0957-0.15670.1055-1.3599-17.505918.282
94.0015-0.5074-0.38590-1.0623.010.1097-0.30010.4447-0.0153-0.41080.0408-0.25090.24970.3011-0.24240.0195-0.08370.0270.08130.136412.0591-23.477610.2506
106.87730.592-3.232.55271.13642.88640.14080.3529-0.0136-0.2789-0.61940.4754-0.421-0.79040.4786-0.34520.0902-0.1170.2694-0.1689-0.0481-5.9022-29.18514.6686
112.15920.08996.01523.64443.16740.3683-0.0143-0.07260.0242-0.1967-0.14110.0211-0.1747-0.08750.1553-0.2980.09570.25430.08450.01380.1391-5.2967-39.6255.3924
123.88092.86322.43473.16262.97710-0.0017-0.28620.24130.3469-0.0161-0.1828-0.20020.0180.0178-0.2331-0.06340.03920.03210.15690.20944.5425-17.4459-20.4442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 28}
2X-RAY DIFFRACTION2{A|29 - 88}
3X-RAY DIFFRACTION3{A|89 - 125}
4X-RAY DIFFRACTION4{A|126 - 300}
5X-RAY DIFFRACTION5{A|301 - 323}
6X-RAY DIFFRACTION6{A|324 - 405}
7X-RAY DIFFRACTION7{A|406 - 491}
8X-RAY DIFFRACTION8{A|492 - 573}
9X-RAY DIFFRACTION9{A|574 - 656}
10X-RAY DIFFRACTION10{A|657 - 713}
11X-RAY DIFFRACTION11{D|1 - 7}
12X-RAY DIFFRACTION12{D|19 - 21}

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