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- PDB-1rc5: CRYSTAL STRUCTURE OF MG(II)-COMPLEX OF RNASE III ENDONUCLEASE DOM... -

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Basic information

Entry
Database: PDB / ID: 1rc5
TitleCRYSTAL STRUCTURE OF MG(II)-COMPLEX OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS AT 2.30 ANGSTROM RESOLUTION
ComponentsRibonuclease III
KeywordsHYDROLASE / RIBONUCLEASE / RNASE III / DOUBLE-STRANDED RNA / RNA INTERFERENCE / ENDONUCLEASE DOMAIN / ENDONUCLEOLYTIC CLEAVAGE
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 motif ...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 motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBlaszczyk, J. / Gan, J. / Ji, X.
Citation
Journal: Structure / Year: 2004
Title: Noncatalytic Assembly of Ribonuclease III with Double-Stranded RNA.
Authors: Blaszczyk, J. / Gan, J. / Tropea, J.E. / Court, D.L. / Waugh, D.S. / Ji, X.
#1: Journal: Structure / Year: 2001
Title: Crystallographic and Modelling Studies of RNase III Suggest a Mechanism for Double-Stranded RNA Cleavage
Authors: Blaszczyk, J. / Tropea, J.E. / Bubunenko, M. / Routzahn, K.M. / Waugh, D.S. / Court, D.L. / Ji, X.
History
DepositionNov 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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 1.4Aug 30, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Remark 999SEQUENCE EXPRESSED WITH A N-TERMINAL GLYCINE RESIDUE, AND WITH SIX-HISTIDINE-TAGGED C-TERMINUS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease III
B: Ribonuclease III
C: Ribonuclease III
D: Ribonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7498
Polymers72,6524
Non-polymers974
Water12,160675
1
A: Ribonuclease III
B: Ribonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3754
Polymers36,3262
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-28 kcal/mol
Surface area14580 Å2
MethodPISA
2
C: Ribonuclease III
D: Ribonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3754
Polymers36,3262
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-27 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.742, 140.856, 49.746
Angle α, β, γ (deg.)90.00, 117.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribonuclease III / RNase III


Mass: 18163.012 Da / Num. of mol.: 4 / Fragment: N-TERMINAL ENDONUCLEASE DOMAIN (RESIDUES 1-147)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: RNC, AQ_946 / Plasmid: PKM803 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O67082, ribonuclease III
#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 675 / Fragment: WATER / 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: 2.08 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, TRIS-HCL, ACETATE, CHLORIDE, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.045 / Wavelength: 1.045 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 10, 2001 / Details: MIRROR
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 24431 / Num. obs: 24431 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.822 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.8929
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.42 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 3.903 / Num. unique all: 2407 / % possible all: 87.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1I4S

1i4s


Resolution: 2.3→30 Å / Num. parameters: 20239 / Num. restraintsaints: 20369 / Isotropic thermal model: ISOTROPIC / Cross valid method: FREE R / σ(F): 4 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER
Details: LEAST-SQUARES REFINEMENT USING THE KONNERT-HENDRICKSON CONJUGATE-GRADIENT ALGORITHM. CNS was also used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 1248 5.4398 %RANDOM
Rwork0.197 ---
obs0.1918 19661 85.1 %-
all-22942 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1975) 201-228
Displacement parametersBiso mean: 34.611 Å2
Refine analyzeLuzzati coordinate error obs: 0.253 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5599
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4929 0 4 675 5608
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.016
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.018
X-RAY DIFFRACTIONs_zero_chiral_vol0.019
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.026
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.019
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.079
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
2.3-2.40.245X-RAY DIFFRACTION243810
2.4-2.510.229X-RAY DIFFRACTION233710
2.51-2.670.205X-RAY DIFFRACTION212710
2.67-2.840.193X-RAY DIFFRACTION235210
2.84-3.050.18X-RAY DIFFRACTION236710
3.05-3.310.176X-RAY DIFFRACTION222410
3.31-3.70.179X-RAY DIFFRACTION227410
3.7-4.630.174X-RAY DIFFRACTION229110
4.63-7.810.194X-RAY DIFFRACTION224710
7.81-300.302X-RAY DIFFRACTION56710

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