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- PDB-3zc0: Structure of AfC3PO - duplex RNA complex -

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Basic information

Entry
Database: PDB / ID: 3zc0
TitleStructure of AfC3PO - duplex RNA complex
Components
  • 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP*GP*UP*CP*GP*AP*AP*UP*U)-3'
  • AFTRAX
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / TRANSLIN / TRAX / RNA INTERFERENCE / RNAI / RNA SILENCING / SIRNA / PASSENGER STRAND / RISC
Function / homology
Function and homology information


sequence-specific DNA binding / identical protein binding / metal ion binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2140 / Translin family / Translin superfamily / Translin family / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Translin
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.982 Å
AuthorsParizotto, E.A. / Lowe, E.D. / Parker, J.S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structural Basis for Duplex RNA Recognition and Cleavage by Archaeoglobus Fulgidus C3Po.
Authors: Parizotto, E.A. / Lowe, E.D. / Parker, J.S.
History
DepositionNov 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 27, 2013Group: Database references
Revision 1.3Mar 20, 2013Group: Database references
Revision 1.4Dec 20, 2023Group: 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_ptnr2_label_alt_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 / _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: AFTRAX
B: AFTRAX
C: AFTRAX
D: AFTRAX
E: AFTRAX
F: AFTRAX
G: AFTRAX
H: AFTRAX
I: AFTRAX
J: AFTRAX
K: AFTRAX
L: AFTRAX
M: 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP*GP*UP*CP*GP*AP*AP*UP*U)-3'
N: 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP*GP*UP*CP*GP*AP*AP*UP*U)-3'
O: 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP*GP*UP*CP*GP*AP*AP*UP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,25131
Polymers288,81815
Non-polymers43316
Water1,54986
1
E: AFTRAX
F: AFTRAX
G: AFTRAX
H: AFTRAX
N: 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP*GP*UP*CP*GP*AP*AP*UP*U)-3'
hetero molecules

I: AFTRAX
J: AFTRAX
K: AFTRAX
L: AFTRAX
O: 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP*GP*UP*CP*GP*AP*AP*UP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,84621
Polymers192,54510
Non-polymers30111
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_664-x+1,-x+y+1,-z-2/31
Buried area29830 Å2
ΔGint-268 kcal/mol
Surface area64110 Å2
MethodPISA
2
A: AFTRAX
B: AFTRAX
C: AFTRAX
D: AFTRAX
M: 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP*GP*UP*CP*GP*AP*AP*UP*U)-3'
hetero molecules

A: AFTRAX
B: AFTRAX
C: AFTRAX
D: AFTRAX
M: 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP*GP*UP*CP*GP*AP*AP*UP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,81120
Polymers192,54510
Non-polymers26510
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area29490 Å2
ΔGint-260.7 kcal/mol
Surface area64880 Å2
MethodPISA
3
I: AFTRAX
J: AFTRAX
K: AFTRAX
L: AFTRAX
O: 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP*GP*UP*CP*GP*AP*AP*UP*U)-3'
hetero molecules

E: AFTRAX
F: AFTRAX
G: AFTRAX
H: AFTRAX
N: 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP*GP*UP*CP*GP*AP*AP*UP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,84621
Polymers192,54510
Non-polymers30111
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_654-x+1,-x+y,-z-2/31
MethodPISA
Unit cell
Length a, b, c (Å)183.060, 183.060, 198.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11M-7-

G

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
13
23
33
14
24
34
15
25
16
26

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN B AND NOT (RESID 76)
211CHAIN F AND NOT (RESID 33 OR RESID 137 OR RESID 164)
311CHAIN J AND NOT (RESID 51 OR RESID 52 OR RESID 58 OR RESID 148 OR RESID 158)
112CHAIN C AND NOT (RESID 137 OR RESID 147 OR RESID 166 OR RESID 188)
212CHAIN G AND NOT (RESID 18 OR RESID 26 OR RESID 65)
312CHAIN K AND NOT (RESID 22 OR RESID 25 OR RESID 72 OR RESID 80)
113CHAIN D AND NOT (RESID 28 OR RESID 68 OR RESID 94)
213CHAIN H AND NOT (RESID 80 OR RESID 140)
313CHAIN L AND NOT (RESID 8 OR RESID 22 OR RESID 100 OR RESID 137 OR RESID 148)
114CHAIN A AND NOT (RESID 64 OR RESID 74 OR RESID 80 OR RESID 151 OR RESSEQ 157:160)
214CHAIN E AND NOT (RESID 22 OR RESID 28 OR RESID 52 OR RESID 110 OR RESID 147 OR RESID 164)
314CHAIN I AND NOT (RESID 44 OR RESID 76 OR...
115CHAIN E AND RESSEQ 158:160
215CHAIN I AND RESSEQ 158:160
116CHAIN M
216CHAIN N

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(-0.49877, 0.866734, -0.000538), (0.866733, 0.49877, 0.001559), (0.001619, 0.000311, -0.999999)-53.6192, -30.699, -66.1373
2given(-0.501134, -0.865369, -0.001105), (-0.865367, 0.50113, 0.002931), (-0.001983, 0.002425, -0.999995)91.466, 96.961, -66.0303
3given(-0.501584, 0.865109, -0.000428), (0.865107, 0.501584, 0.001872), (0.001834, 0.000569, -0.999998)-53.2687, -30.849, -66.0885
4given(-0.499811, -0.866134, -0.000174), (-0.866134, 0.499811, 0.001252), (-0.000997, 0.000776, -0.999999)91.4726, 96.9959, -65.9615
5given(-0.499873, 0.866097, -0.001895), (0.866098, 0.499875, 0.000608), (0.001474, -0.001337, -0.999998)-53.4904, -30.8277, -65.938
6given(-0.501368, -0.865231, -0.002249), (-0.865233, 0.50137, -0.000515), (0.001573, 0.001687, -0.999997)91.4271, 96.7753, -66.2683
7given(-0.501291, 0.865278, -0.001383), (0.865277, 0.501292, 0.001353), (0.001864, -0.000519, -0.999998)-53.3649, -30.9244, -66.0284
8given(-0.501001, -0.865447, -0.000121), (-0.865443, 0.500999, 0.00281), (-0.002371, 0.001512, -0.999996)91.4922, 96.9504, -65.9664
9given(-0.492322, 0.870272, 0.015679), (-0.869876, -0.491306, -0.043984), (-0.030575, -0.035293, 0.998909)38.4147, 187.195, 2.73425
10given(-0.502209, 0.864728, 0.00552), (0.864727, 0.502231, -0.003508), (-0.005806, 0.003012, -0.999979)-52.8078, -31.3942, -66.1703

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Components

#1: Protein
AFTRAX / AF2260


Mass: 22799.396 Da / Num. of mol.: 12 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Strain: VC-16
Description: DSMZ, GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES
Plasmid: MODIFIED PET-17B (PTWO-E) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O28024
#2: RNA chain 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP*GP*UP*CP*GP*AP*AP*UP*U)-3'


Mass: 5075.040 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCRYSTALLISED AFTRAX MOLECULE CONTAINS D114A CATALYTIC MUTATION AND REMAINDER OF N-TERMINAL TAG (GLY- ...CRYSTALLISED AFTRAX MOLECULE CONTAINS D114A CATALYTIC MUTATION AND REMAINDER OF N-TERMINAL TAG (GLY-PRO-HIS) SYNTHETIC CONSTRUCT

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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: 3.3 Å3/Da / Density % sol: 63 % / Description: DATA COLLECTION PHI WIDTH EQUALS 0.15 DEGREES
Crystal growpH: 8
Details: 2.7 M 1,6-HEXANEDIOL, 200 MM AMMONIUM CHLORIDE, 10 MM MGCL2, 50 MM HEPES PH 8.0, 5 MM DTT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2011
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.98→123.78 Å / Num. obs: 78522 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 66.77 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.6
Reflection shellResolution: 2.98→3.06 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
XDSdata reduction
xia2data scaling
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZC1

3zc1


Resolution: 2.982→83.091 Å / SU ML: 0.38 / σ(F): 1.22 / Phase error: 32.52 / Stereochemistry target values: ML
Details: USED PHENIX.REFINE VERSION 1.8. PROTEIN CHAINS COMPLETE EXCEPT 79 OUT OF 2352 SIDE CHAINS MODELLED AS ALANINE STUBS AND 5 TO 9 RESIDUES AT EACH C TERMINUS, MISSING DUE TO INSUFFICIENT ...Details: USED PHENIX.REFINE VERSION 1.8. PROTEIN CHAINS COMPLETE EXCEPT 79 OUT OF 2352 SIDE CHAINS MODELLED AS ALANINE STUBS AND 5 TO 9 RESIDUES AT EACH C TERMINUS, MISSING DUE TO INSUFFICIENT ELECTRON DENSITY. RNA CHAINS M, N AND O ARE EACH MODELLED AS TWO COMPLETE OVERLAPPING CONFORMERS, A AND B, OF FIXED OCCUPANCY 0.5. CONFORMERS MA, NA AND OB COMPRISE NUCLEOTIDES 1 TO 14 AND CONFORMERS MB, NB AND OA COMPRISE NUCLEOTIDES 2 TO 15. BECAUSE RNA DUPLEXES ARE FORMED BETWEEN SPECIFIC PAIRS OF CONFORMERS, APPROPRIATE MEASURES SUCH AS EXEMPTION FROM SYMMETRY RELATED INTERACTIONS WERE TAKEN TO PREVENT INCORRECT BASE PAIR CLASHES DURING REFINEMENT. MAGNESIUM COORDINATION INTERACTIONS WERE BUILT USING PHENIX.METAL_ COORDINATION.
RfactorNum. reflection% reflection
Rfree0.2572 7620 5 %
Rwork0.2078 --
obs0.2103 78400 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.38 Å2
Refinement stepCycle: LAST / Resolution: 2.982→83.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18036 903 16 86 19041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02120373
X-RAY DIFFRACTIONf_angle_d1.24227631
X-RAY DIFFRACTIONf_dihedral_angle_d18.8987953
X-RAY DIFFRACTIONf_chiral_restr0.0843191
X-RAY DIFFRACTIONf_plane_restr0.0053242
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1485X-RAY DIFFRACTIONPOSITIONAL
12F1485X-RAY DIFFRACTIONPOSITIONAL0.038
13J1439X-RAY DIFFRACTIONPOSITIONAL0.038
21C1430X-RAY DIFFRACTIONPOSITIONAL
22G1430X-RAY DIFFRACTIONPOSITIONAL0.035
23K1416X-RAY DIFFRACTIONPOSITIONAL0.034
31D1441X-RAY DIFFRACTIONPOSITIONAL
32H1441X-RAY DIFFRACTIONPOSITIONAL0.034
33L1401X-RAY DIFFRACTIONPOSITIONAL0.032
41A1384X-RAY DIFFRACTIONPOSITIONAL
42E1384X-RAY DIFFRACTIONPOSITIONAL0.036
43I1379X-RAY DIFFRACTIONPOSITIONAL0.036
51E20X-RAY DIFFRACTIONPOSITIONAL
52I20X-RAY DIFFRACTIONPOSITIONAL0.024
61M560X-RAY DIFFRACTIONPOSITIONAL
62N560X-RAY DIFFRACTIONPOSITIONAL0.016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9816-3.01550.36872480.32514838X-RAY DIFFRACTION100
3.0155-3.0510.38272670.31394798X-RAY DIFFRACTION100
3.051-3.08820.32012570.28744780X-RAY DIFFRACTION100
3.0882-3.12730.32552600.2814773X-RAY DIFFRACTION100
3.1273-3.16850.34282730.28674811X-RAY DIFFRACTION100
3.1685-3.21190.32853100.2734744X-RAY DIFFRACTION100
3.2119-3.25780.31192320.27654766X-RAY DIFFRACTION100
3.2578-3.30640.33092040.25664857X-RAY DIFFRACTION100
3.3064-3.3580.32662640.26674709X-RAY DIFFRACTION100
3.358-3.41310.3442430.26934859X-RAY DIFFRACTION100
3.4131-3.4720.32472220.25794772X-RAY DIFFRACTION100
3.472-3.53510.30932580.24544828X-RAY DIFFRACTION100
3.5351-3.60310.2662350.23094791X-RAY DIFFRACTION100
3.6031-3.67660.29422030.22274785X-RAY DIFFRACTION100
3.6766-3.75660.28272410.21624820X-RAY DIFFRACTION100
3.7566-3.8440.2393000.19794721X-RAY DIFFRACTION100
3.844-3.94010.25532620.19024809X-RAY DIFFRACTION100
3.9401-4.04660.26172750.20624782X-RAY DIFFRACTION100
4.0466-4.16570.23162990.19074750X-RAY DIFFRACTION100
4.1657-4.30010.21362400.17344788X-RAY DIFFRACTION100
4.3001-4.45380.2092690.16634804X-RAY DIFFRACTION100
4.4538-4.63210.23032590.17774767X-RAY DIFFRACTION100
4.6321-4.84290.20932250.16954833X-RAY DIFFRACTION100
4.8429-5.09820.20132510.16474780X-RAY DIFFRACTION100
5.0982-5.41760.24992470.184773X-RAY DIFFRACTION100
5.4176-5.83580.25072200.19534840X-RAY DIFFRACTION100
5.8358-6.42290.27662760.19644773X-RAY DIFFRACTION100
6.4229-7.35180.22622510.1814780X-RAY DIFFRACTION100
7.3518-9.26050.18282830.15954745X-RAY DIFFRACTION100
9.2605-83.12340.2472460.2194736X-RAY DIFFRACTION98

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