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Basic information

Entry
Database: PDB / ID: 4ieg
TitleStructure and interactions of the RNA-dependent RNA polymerase from bacteriophage phi12 (P1 crystal form)
ComponentsRNA-dependent RNA polymerase P2
KeywordsTRANSFERASE / RNA-directed RNA polymerase
Function / homologyCystovirus, RNA-directed RNA polymerase / RNA-directed RNA polymerase, bacteriophage, catalytic domain / RdRp of RNA-containing bacteriophages catalytic domain profile. / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA/RNA polymerase superfamily / metal ion binding / RNA-directed RNA polymerase
Function and homology information
Biological speciesPseudomonas phage phi12 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRen, Z. / Franklin, M.C. / Ghose, R.
CitationJournal: Proteins / Year: 2013
Title: Structure of the RNA-directed RNA Polymerase from the cystovirus 12.
Authors: Ren, Z. / C Franklin, M. / Ghose, R.
History
DepositionDec 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_asym_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_ref_seq_dif.details / _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: RNA-dependent RNA polymerase P2
B: RNA-dependent RNA polymerase P2
C: RNA-dependent RNA polymerase P2
D: RNA-dependent RNA polymerase P2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,9398
Polymers301,8414
Non-polymers974
Water29,8151655
1
A: RNA-dependent RNA polymerase P2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4852
Polymers75,4601
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-dependent RNA polymerase P2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4852
Polymers75,4601
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA-dependent RNA polymerase P2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4852
Polymers75,4601
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RNA-dependent RNA polymerase P2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4852
Polymers75,4601
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.874, 94.470, 96.481
Angle α, β, γ (deg.)75.16, 63.11, 83.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
RNA-dependent RNA polymerase P2


Mass: 75460.359 Da / Num. of mol.: 4 / Mutation: M2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage phi12 (virus) / Gene: P2 / Plasmid: pPG27 / Production host: Escherichia coli (E. coli) / Strain (production host): BL12(DE3) / References: UniProt: Q94M06
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1655 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Mg formate 20% PEG 3350, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 3, 2012
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 156487 / Num. obs: 144893 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.8
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 2.9 / Num. unique all: 7802 / % possible all: 87.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GZK

4gzk


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.882 / SU B: 14.902 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.329 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27836 7276 5 %RANDOM
Rwork0.2172 ---
all0.22 156991 --
obs0.22025 137611 92.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.467 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20.62 Å2-0.17 Å2
2--0.57 Å2-0.53 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20846 0 4 1655 22505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02221535
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215005
X-RAY DIFFRACTIONr_angle_refined_deg1.11.94729192
X-RAY DIFFRACTIONr_angle_other_deg0.817336256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64652606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41823.4821097
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.926153599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.03215173
X-RAY DIFFRACTIONr_chiral_restr0.0640.23043
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02124146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024691
X-RAY DIFFRACTIONr_mcbond_it0.3661.512920
X-RAY DIFFRACTIONr_mcbond_other0.0741.55188
X-RAY DIFFRACTIONr_mcangle_it0.685220898
X-RAY DIFFRACTIONr_scbond_it1.11238615
X-RAY DIFFRACTIONr_scangle_it1.8184.58274
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 482 -
Rwork0.25 9164 -
obs--83.31 %
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)
10.6089-0.1850.0910.7628-0.1340.49750.03710.0180.0130.0332-0.03840.08590.059-0.18830.00130.024-0.02790.01730.0856-0.01390.027127.296328.35263.8457
20.35590.05090.00460.4670.03540.81120.0893-0.03650.10660.0105-0.0185-0.0325-0.09180.1496-0.07080.0604-0.02550.05050.0329-0.02110.052669.665963.18679.1204
30.70860.0371-0.12760.6309-0.13580.47580.0620.0319-0.08820.0256-0.01640.0728-0.095-0.1077-0.04560.04560.02070.010.02820.00440.030471.214120.5693-30.1248
40.7327-0.43020.03380.77-0.22860.58670.13920.0408-0.1486-0.0885-0.0930.07550.1030.1695-0.04620.10520.0391-0.05680.0508-0.02040.041137.341780.3668-35.6582
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 659
2X-RAY DIFFRACTION2B11 - 659
3X-RAY DIFFRACTION3C10 - 659
4X-RAY DIFFRACTION4D10 - 659

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