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- PDB-3zc1: Crystal structure of AfC3PO -

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Basic information

Entry
Database: PDB / ID: 3zc1
TitleCrystal structure of AfC3PO
ComponentsAFTRAX
KeywordsHYDROLASE / 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
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.269 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 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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: AFTRAX
B: AFTRAX
C: AFTRAX
D: AFTRAX
E: AFTRAX
F: AFTRAX
G: AFTRAX
H: AFTRAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,86913
Polymers182,7478
Non-polymers1225
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25050 Å2
ΔGint-161.3 kcal/mol
Surface area60860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.310, 183.310, 111.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND NOT (RESID 7 OR RESID 47 OR...
211CHAIN E
112CHAIN B AND NOT (RESID 7 OR RESID 47 OR RESID 148 OR RESID 165 OR RESID 179)
212CHAIN F
113CHAIN C AND NOT (RESID 7 OR RESID 147 OR RESID 166)
213CHAIN G
114CHAIN D AND NOT (RESID 7 OR RESID 12 OR RESID 28 OR RESID 42 OR RESID 52 OR RESID 148 OR RESID 164)
214CHAIN H

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(-0.369385, -0.476777, 0.797645), (-0.478362, -0.638332, -0.603077), (0.796696, -0.604331, 0.007718)10.1696, 96.3558, 49.7779
2given(-0.362161, -0.471693, 0.803956), (-0.474901, -0.648794, -0.594588), (0.802065, -0.597136, 0.01096)9.82556, 96.3543, 49.4169
3given(-0.350248, -0.482835, 0.802619), (-0.483557, -0.640665, -0.596423), (0.802184, -0.597008, -0.009086)10.4637, 96.5685, 50.3049
4given(-0.367866, -0.472221, 0.80105), (-0.480078, -0.64132, -0.598526), (0.796367, -0.604744, 0.009217)10.3976, 96.5798, 49.7541

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Components

#1: Protein
AFTRAX / AF2260


Mass: 22843.406 Da / Num. of mol.: 8
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: PTWO-E / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O28024
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCRYSTALLISED AFTRAX MOLECULE CONTAINS REMAINDER OF N- TERMINAL TAG (GLY-PRO-HIS)

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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: 2.6 Å3/Da / Density % sol: 52 %
Description: A PRELIMARY MODEL WAS BUILT USING SAD DATA TO 3.41 ANGSTROMS. THIS WAS THEN USED TO SOLVE BY MR A 2.98 ANGSTROM DATASET OF A DIFFERENT CRYSTAL FORM, WHOSE REFINED MODEL WAS THEN USED TO ...Description: A PRELIMARY MODEL WAS BUILT USING SAD DATA TO 3.41 ANGSTROMS. THIS WAS THEN USED TO SOLVE BY MR A 2.98 ANGSTROM DATASET OF A DIFFERENT CRYSTAL FORM, WHOSE REFINED MODEL WAS THEN USED TO SOLVE BY MR THE NATIVE DATASET.
Crystal growpH: 5.5
Details: 9.5 - 10 % PEG 3K, 100 MM KCL, 200 MM MGCL2, 40 MM SODIUM CACODYLATE PH 5.5, 5 MM DTT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 1, 2010 / Details: COMPOUND REFRACTIVE LENSES
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.27→70.75 Å / Num. obs: 29895 / % possible obs: 99.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 106.14 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.5
Reflection shellResolution: 3.27→3.35 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
Cootmodel building
xia2data reduction
xia2data scaling
SCALAdata scaling
SnBphasing
autoSHARPphasing
PHENIXAUTOBUILDphasing
Cootphasing
PHENIXphasing
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZC0

3zc0


Resolution: 3.269→53.56 Å / SU ML: 1.18 / σ(F): 1.35 / Phase error: 31.98 / Stereochemistry target values: ML
Details: USED PHENIX.REFINE VERSION 1.7.2. PROTEIN CHAINS COMPLETE EXCEPT 110 OUT OF 1568 SIDE CHAINS MODELLED AS ALANINE STUBS AND 6 TO 9 RESIDUES AT EACH C TERMINUS, MISSING DUE TO INSUFFICIENT ...Details: USED PHENIX.REFINE VERSION 1.7.2. PROTEIN CHAINS COMPLETE EXCEPT 110 OUT OF 1568 SIDE CHAINS MODELLED AS ALANINE STUBS AND 6 TO 9 RESIDUES AT EACH C TERMINUS, MISSING DUE TO INSUFFICIENT ELECTRON DENSITY. MAGNESIUM COORDINATION INTERACTIONS WERE BUILT USING PHENIX.METAL_ COORDINATION.
RfactorNum. reflection% reflection
Rfree0.2813 3776 6.8 %
Rwork0.2205 --
obs0.2246 29852 99.88 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.212 Å2 / ksol: 0.288 e/Å3
Displacement parametersBiso mean: 103.54 Å2
Baniso -1Baniso -2Baniso -3
1--15.74 Å20 Å20 Å2
2---15.74 Å20 Å2
3---31.4801 Å2
Refinement stepCycle: LAST / Resolution: 3.269→53.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11807 0 5 8 11820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111979
X-RAY DIFFRACTIONf_angle_d1.27916123
X-RAY DIFFRACTIONf_dihedral_angle_d20.1984486
X-RAY DIFFRACTIONf_chiral_restr0.0831851
X-RAY DIFFRACTIONf_plane_restr0.0042080
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1402X-RAY DIFFRACTIONPOSITIONAL
12E1402X-RAY DIFFRACTIONPOSITIONAL0.045
21B1418X-RAY DIFFRACTIONPOSITIONAL
22F1418X-RAY DIFFRACTIONPOSITIONAL0.05
31C1408X-RAY DIFFRACTIONPOSITIONAL
32G1408X-RAY DIFFRACTIONPOSITIONAL0.05
41D1355X-RAY DIFFRACTIONPOSITIONAL
42H1355X-RAY DIFFRACTIONPOSITIONAL0.048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2694-3.31080.45611360.3861932X-RAY DIFFRACTION100
3.3108-3.35430.38861420.35421952X-RAY DIFFRACTION100
3.3543-3.40030.40481400.33571935X-RAY DIFFRACTION100
3.4003-3.44880.41991320.32311920X-RAY DIFFRACTION100
3.4488-3.50030.34621410.3091928X-RAY DIFFRACTION100
3.5003-3.5550.38331380.29251930X-RAY DIFFRACTION100
3.555-3.61330.38111350.3011941X-RAY DIFFRACTION100
3.6133-3.67560.41271370.29231941X-RAY DIFFRACTION100
3.6756-3.74240.28161380.25231931X-RAY DIFFRACTION100
3.7424-3.81430.33651420.23731936X-RAY DIFFRACTION100
3.8143-3.89220.32581390.23721931X-RAY DIFFRACTION100
3.8922-3.97680.31141440.23451941X-RAY DIFFRACTION100
3.9768-4.06930.27131370.21361916X-RAY DIFFRACTION100
4.0693-4.1710.261400.1971951X-RAY DIFFRACTION100
4.171-4.28370.27781410.22231944X-RAY DIFFRACTION100
4.2837-4.40970.29151370.21681906X-RAY DIFFRACTION100
4.4097-4.5520.31131410.20641949X-RAY DIFFRACTION100
4.552-4.71460.25091410.20431942X-RAY DIFFRACTION100
4.7146-4.90320.31681400.21131906X-RAY DIFFRACTION100
4.9032-5.12620.28651400.22641947X-RAY DIFFRACTION100
5.1262-5.39620.3381440.24761938X-RAY DIFFRACTION100
5.3962-5.73390.32271430.26481916X-RAY DIFFRACTION100
5.7339-6.17610.34261420.22731947X-RAY DIFFRACTION100
6.1761-6.79650.24191420.21381930X-RAY DIFFRACTION100
6.7965-7.77740.21841370.16761943X-RAY DIFFRACTION100
7.7774-9.78890.17561440.1381915X-RAY DIFFRACTION99
9.7889-53.56730.22511430.19441923X-RAY DIFFRACTION99

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