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- PDB-4m30: Crystal structure of RNASE III complexed with double-stranded RNA... -

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Basic information

Entry
Database: PDB / ID: 4m30
TitleCrystal structure of RNASE III complexed with double-stranded RNA AND AMP (TYPE II CLEAVAGE)
Components
  • RNA12
  • Ribonuclease 3
KeywordsHYDROLASE/RNA / RNase III / hydrolase / dsRNA / RNA binding / RNA processing / HYDROLASE-RNA complex
Function / homology
Function and homology information


ribonuclease III / ribonuclease III activity / tRNA processing / RNA processing / mRNA processing / rRNA processing / double-stranded RNA binding / regulation of gene expression / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double Stranded RNA Binding Domain - #20 ...Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / RNA / RNA (> 10) / Ribonuclease 3
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsGan, J. / Liang, Y.-H. / Shaw, G.X. / Tropea, J.E. / Waugh, D.S. / Ji, X.
CitationJournal: Annu. Rev. Genet. / Year: 2013
Title: RNase III: Genetics and Function; Structure and Mechanism.
Authors: Court, D.L. / Gan, J. / Liang, Y.H. / Shaw, G.X. / Tropea, J.E. / Costantino, N. / Waugh, D.S. / Ji, X.
History
DepositionAug 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_auth_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.0May 29, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease 3
B: Ribonuclease 3
C: RNA12
D: RNA12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,62816
Polymers69,5974
Non-polymers1,03112
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10880 Å2
ΔGint-171 kcal/mol
Surface area27160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.104, 81.104, 223.962
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCD

#1: Protein Ribonuclease 3 / Ribonuclease III / RNase III


Mass: 26147.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_946, rnc / Plasmid: pHPK1409 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus-RIL / References: UniProt: O67082, ribonuclease III
#2: RNA chain RNA12


Mass: 8651.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Cleavage product of a R1.1 RNA derivative

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Non-polymers , 4 types, 82 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 3.06 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 70% (v/v) MPD in 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 26, 2006 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 28418 / Num. obs: 28418 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 74.45 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.003 / Net I/σ(I): 18.569
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.5-2.592.10.2982.2219930.76966.8
2.59-2.693.60.2823.2528070.86793.3
2.69-2.825.40.2485.829701.00799
2.82-2.966.50.17610.0929391.06899.3
2.96-3.157.30.11816.9830341.02299.4
3.15-3.397.70.08722.2829850.96799.6
3.39-3.7380.05932.0830131.06899.1
3.73-4.277.50.05327.7229690.98396.6
4.27-5.386.90.06619.4428910.98893.5
5.38-306.80.07616.3128171.00686

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RC7

1rc7


Resolution: 2.501→29.116 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 988 3.48 %random
Rwork0.1979 ---
obs0.2001 28395 93.31 %-
all-30431 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.936 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 142.78 Å2 / Biso mean: 80.2303 Å2 / Biso min: 46.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.1766 Å20 Å20 Å2
2---0.1766 Å2-0 Å2
3---0.3532 Å2
Refinement stepCycle: LAST / Resolution: 2.501→29.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3659 1152 63 70 4944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015117
X-RAY DIFFRACTIONf_angle_d1.0527079
X-RAY DIFFRACTIONf_chiral_restr0.069821
X-RAY DIFFRACTIONf_plane_restr0.004679
X-RAY DIFFRACTIONf_dihedral_angle_d15.2752115
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.5006-2.63240.33071090.270730503159305074
2.6324-2.79720.3151460.266740454191404598
2.7972-3.01290.3281460.24840994245409999
3.0129-3.31580.29561510.2194412342744123100
3.3158-3.79470.26851510.202641594310415999
3.7947-4.77750.24581460.16440114157401195
4.7775-29.11810.23221390.192239204059392089

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