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- PDB-5g5s: Structure of the Argonaute protein from Methanocaldcoccus janaschii -

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Basic information

Entry
Database: PDB / ID: 5g5s
TitleStructure of the Argonaute protein from Methanocaldcoccus janaschii
ComponentsARGONAUTE
KeywordsHYDROLASE / 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 / metal ion binding
Similarity search - Function
Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Biological speciesMETHANOCALDOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.29 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1023
Polymers84,9551
Non-polymers1462
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.477, 104.932, 115.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ARGONAUTE


Mass: 84955.227 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.25 Å3/Da / Density % sol: 0.43 % / Description: NONE
Crystal growDetails: 0.1 M TRI- SODIUM CITRATE, 8 % (W/V) POLYETHYLENE GLYCOL 4000 AND 10-12 % (V/V) ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→49.1 Å / Num. obs: 34953 / % possible obs: 1 % / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 74.44 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.8
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.43 / Mean I/σ(I) obs: 1.19 / % possible all: 1

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
CRANKphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.29→49.12 Å / Cor.coef. Fo:Fc: 0.9496 / Cor.coef. Fo:Fc free: 0.9445 / SU R Cruickshank DPI: 0.319 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.305 / SU Rfree Blow DPI: 0.21 / SU Rfree Cruickshank DPI: 0.216
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=5569. 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=5569. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=1. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 1796 5.14 %RANDOM
Rwork0.2097 ---
obs0.2112 34948 98.86 %-
Displacement parametersBiso mean: 90.56 Å2
Baniso -1Baniso -2Baniso -3
1--4.575 Å20 Å20 Å2
2--11.1547 Å20 Å2
3----6.5797 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 2.29→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5541 0 9 2 5552
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095704HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.117748HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1936SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes142HARMONIC2
X-RAY DIFFRACTIONt_gen_planes816HARMONIC5
X-RAY DIFFRACTIONt_it5704HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion19.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion764SEMIHARMONIC5
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_contact6253SEMIHARMONIC4
LS refinement shellResolution: 2.29→2.36 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.255 117 4.71 %
Rwork0.2375 2369 -
all0.2383 2486 -
obs--98.86 %
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)
15.8416-2.3064-3.69574.32621.34926.30560.206-0.3541-1.0670.07380.12180.87760.9160.1644-0.3278-0.14060.0457-0.3066-0.3289-0.04850.1753-25.9747-27.8771-11.3175
27.77541.83790.281310.9298-2.08892.75270.31450.80170.6701-0.3636-0.4145-0.6207-0.39220.61980.1-0.16350.0986-0.0332-0.05460.08140.16013.5741-14.7427-16.9047
36.0129-0.56981.80491.9509-0.72551.85170.61640.8444-0.8293-0.6491-0.282-0.00950.45330.5248-0.3345-0.0550.179-0.1203-0.1712-0.0899-0.0428-12.0847-19.2931-20.3637
44.775-4.0391-5.41273.78222.97485.50460.114-1.41780.5857-0.39471.0038-0.7789-0.94611.5532-1.1178-0.0494-0.12620.08880.181-0.1688-0.3242-19.190414.2439-28.5722
56.4139-0.551-0.45211.36952.26692.4917-0.1287-0.82040.5050.24170.3847-0.4102-0.12980.5194-0.256-0.0053-0.02080.13410.1265-0.0581-0.362-21.102811.2158-23.6206
63.8868-0.6659-1.98053.3032-0.67834.18960.64170.5267-0.4781-0.88360.07390.63090.529-0.1454-0.7156-0.1817-0.0274-0.3636-0.2242-0.07860.1802-32.7512-17.6377-19.9887
76.96772.31910.30922.6268-2.5192.49260.1332-1.0562-0.32030.17940.16270.8464-0.0414-0.8395-0.2959-0.26970.0010.11470.31080.00090.1711-49.794-0.02059.5664
86.5402-0.32840.37474.325-1.16163.0862-0.0917-0.11371.0437-0.1321-0.03390.6523-0.74-0.67450.1256-0.13790.2213-0.0584-0.2201-0.08410.1591-45.701516.3949-4.0537
93.2627-0.18171.28824.8776-0.05812.43940.0893-0.19680.1997-0.11910.0162-0.3395-0.26060.2057-0.1055-0.2207-0.0762-0.021-0.0848-0.0002-0.1646-17.1293.02225.0245
101.63930.10760.51952.61320.62733.23910.3095-0.2005-0.4136-0.0143-0.05180.15550.095-0.129-0.2577-0.1803-0.0406-0.1166-0.10910.07420.0483-24.9355-11.3959-0.7549
111.711-3.3772-2.92642.85771.7013.46610.14020.3109-0.2288-0.3243-0.16790.15320.2609-0.55220.0277-0.1860.0311-0.0766-0.0459-0.1140.0737-39.6304-0.2546-4.7962
124.75150.46380.67013.13971.10382.8178-0.043-0.11610.7047-0.3826-0.10140.236-0.86230.00680.14440.0259-0.009-0.0181-0.08-0.03210.0206-28.929810.8917-1.5606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|-1 - 20}
2X-RAY DIFFRACTION2{A|21 - 61}
3X-RAY DIFFRACTION3{A|62 - 158}
4X-RAY DIFFRACTION4{A|159 - 232}
5X-RAY DIFFRACTION5{A|233 - 262}
6X-RAY DIFFRACTION6{A|263 - 308}
7X-RAY DIFFRACTION7{A|309 - 345}
8X-RAY DIFFRACTION8{A|346 - 495}
9X-RAY DIFFRACTION9{A|496 - 582}
10X-RAY DIFFRACTION10{A|583 - 667}
11X-RAY DIFFRACTION11{A|668 - 679}
12X-RAY DIFFRACTION12{A|680 - 713}

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