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- PDB-6jxm: Crystal Structure of phi29 pRNA domain II -

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Basic information

Entry
Database: PDB / ID: 6jxm
TitleCrystal Structure of phi29 pRNA domain II
ComponentsRNA (97-mer)
KeywordsRNA / phi29 bacteriophage
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesBacillus virus phi29
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsCai, R. / Price, I.R. / Ding, F. / Wu, F. / Chen, T. / Zhang, Y. / Liu, G. / Jardine, P.J. / Lu, C. / Ke, A.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31300603 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: ATP/ADP modulates gp16-pRNA conformational change in the Phi29 DNA packaging motor.
Authors: Cai, R. / Price, I.R. / Ding, F. / Wu, F. / Chen, T. / Zhang, Y. / Liu, G. / Jardine, P.J. / Lu, C. / Ke, A.
History
DepositionApr 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: RNA (97-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,60823
Polymers31,3781
Non-polymers2,23022
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-199 kcal/mol
Surface area16470 Å2
Unit cell
Length a, b, c (Å)120.178, 120.178, 187.494
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: RNA chain RNA (97-mer) / pRNA


Mass: 31377.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus virus phi29 / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Ba

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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: 5.39 Å3/Da / Density % sol: 77.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.12 mM spermine, 5 mM cobalt hexamine, 10%(+/-)-2-methyl-2,4-pentanediol (MPD), 62 mM potassium chloride, 30 mM barium chloride, 40 mM pH 6 Na cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.606 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.606 Å / Relative weight: 1
ReflectionResolution: 3.32→101.18 Å / Num. obs: 10506 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rpim(I) all: 0.041 / Net I/σ(I): 13.9
Reflection shellResolution: 3.32→3.59 Å / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.029

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MGM

4mgm


Resolution: 3.32→101.18 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.932 / SU B: 25.778 / SU ML: 0.373 / Cross valid method: THROUGHOUT / ESU R: 1.178 / ESU R Free: 0.436 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26515 1034 10 %RANDOM
Rwork0.22291 ---
obs0.22702 9296 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 152.093 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.55 Å2
Refinement stepCycle: 1 / Resolution: 3.32→101.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2077 22 0 2099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0112323
X-RAY DIFFRACTIONr_bond_other_d0.0040.02951
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.2743619
X-RAY DIFFRACTIONr_angle_other_deg1.56132309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021168
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02525
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it14.00116.1052322
X-RAY DIFFRACTIONr_scbond_other1416.1092323
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other21.03824.1693619
X-RAY DIFFRACTIONr_long_range_B_refined22.9413184
X-RAY DIFFRACTIONr_long_range_B_other22.9383185
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.321→3.407 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 64 -
Rwork0.404 570 -
obs--83.31 %

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