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- PDB-1n35: lambda3 elongation complex with four phosphodiester bond formed -

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Basic information

Entry
Database: PDB / ID: 1n35
Titlelambda3 elongation complex with four phosphodiester bond formed
Components
  • 5'-R(*AP*UP*UP*AP*GP*CP*CP*CP*CP*C)-3'
  • 5'-R(P*GP*GP*GP*GP*G)-3'
  • Minor core protein lambda 3
KeywordsTRANSFERASE/RNA / RNA polymerase / right hand configuration / bracelet / TRANSFERASE-RNA COMPLEX
Function / homology
Function and homology information


viral genome replication / viral nucleocapsid / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / RNA binding
Similarity search - Function
RNA-directed RNA polymerase lambda-3 / RNA-directed RNA polymerase lambda-3 / Reovirus RNA-dependent RNA polymerase lambda 3 / Reovirus RNA-dependent RNA polymerase lambda 3 / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE / : / RNA / RNA-directed RNA polymerase lambda-3 / RNA-directed RNA polymerase lambda-3
Similarity search - Component
Biological speciesMammalian orthoreovirus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTao, Y. / Farsetta, D.L. / Nibert, M.L. / Harrison, S.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: RNA Synthesis in a Cage--Structural Studies of Reovirus Polymerase [lambda] 3
Authors: Tao, Y. / Farsetta, D.L. / Nibert, M.L. / Harrison, S.C.
History
DepositionOct 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-R(P*GP*GP*GP*GP*G)-3'
C: 5'-R(*AP*UP*UP*AP*GP*CP*CP*CP*CP*C)-3'
A: Minor core protein lambda 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,7138
Polymers147,2023
Non-polymers1,5115
Water6,305350
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.883, 85.013, 249.294
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 2 types, 2 molecules BC

#1: RNA chain 5'-R(P*GP*GP*GP*GP*G)-3'


Mass: 1681.072 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain 5'-R(*AP*UP*UP*AP*GP*CP*CP*CP*CP*C)-3'


Mass: 3096.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: AUUAGC, Ordered from Dharmacon

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Protein , 1 types, 1 molecules A

#3: Protein Minor core protein lambda 3 / lambda3


Mass: 142423.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammalian orthoreovirus 3 / Genus: Orthoreovirus / Species: Mammalian orthoreovirus / Strain: Dearing / Gene: L1 / Plasmid: pFastbac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 / References: UniProt: P17378, UniProt: P0CK31*PLUS

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Non-polymers , 3 types, 355 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CH1 / 3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG4000, NaCl, HEPES, glycerol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG400011
2NaClSodium chloride11
3HEPES11
4glycerol11
5PEG400012
6NaClSodium chloride12
7HEPES12
8glycerol12
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18.7 mg/mlprotein1drop
250 mMsodium HEPES1droppH7.8
310 %glycerol1drop
4150 mM1dropNaCl
510 mMdithiothreitol1drop
60.02 %1dropNaN3
77.5 %PEG80001reservoir
810 %1reservoir
90.1 Msodium HEPES1reservoirpH7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.948 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 48139 / Num. obs: 48139 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.5 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2 / Num. unique all: 3986 / % possible all: 75.3
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 3-4
Reflection shell
*PLUS
% possible obs: 75.3 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: lambda3 native structure

Resolution: 2.5→43.01 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2358160.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2581 5.4 %RANDOM
Rwork0.207 ---
obs0.207 47743 89.9 %-
all-47743 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.2565 Å2 / ksol: 0.345166 e/Å3
Displacement parametersBiso mean: 36.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.7 Å20 Å20 Å2
2--5.04 Å20 Å2
3---0.66 Å2
Refine analyzeLuzzati coordinate error free: 0.38 Å / Luzzati sigma a free: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.5→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9987 282 86 350 10705
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d1.1
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.318 113 2.8 %
Rwork0.29 3880 -
obs--76.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4MGP_NTP_DEOXY_XPMGP_NTP_DEOXY_XP
X-RAY DIFFRACTION5ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.489
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1

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