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- PDB-1i4s: CRYSTAL STRUCTURE OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX A... -

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Basic information

Entry
Database: PDB / ID: 1i4s
TitleCRYSTAL STRUCTURE OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS AT 2.15 ANGSTROM RESOLUTION
ComponentsRIBONUCLEASE III
KeywordsHYDROLASE / RIBONUCLEASE / RNASE III / DOUBLE-STRANDED RNA / CATALYTIC DOMAIN / 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 / identical protein binding / metal ion binding / cytoplasm
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 / MIR / Resolution: 2.15 Å
AuthorsBlaszczyk, J. / Ji, X.
CitationJournal: Structure / Year: 2001
Title: Crystallographic and modeling 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
DepositionFeb 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE III
B: RIBONUCLEASE III


Theoretical massNumber of molelcules
Total (without water)34,5542
Polymers34,5542
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-13 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.157, 51.188, 123.468
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RIBONUCLEASE III / RNASE III


Mass: 17277.078 Da / Num. of mol.: 2 / Fragment: N-TERMINAL ENDONUCLEASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: PKM803 / Production host: Escherichia coli (E. coli) / References: UniProt: O67082, ribonuclease III
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.011 Å3/Da / Density % sol: 36.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, TRIS-HCL, ACETATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98789, 1.01000, 1.03473, 1.04008
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2000 / Details: MIRROR
RadiationMonochromator: SILICON 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.987891
21.011
31.034731
41.040081
ReflectionResolution: 2.15→40 Å / Num. all: 16542 / Num. obs: 16542 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.161 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 23.376
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4.025 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.258 / Num. unique all: 1621 / % possible all: 99.9

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Processing

Software
NameClassification
SHARPphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR
Starting model: NONE

Resolution: 2.15→30 Å / Num. parameters: 9323 / Num. restraintsaints: 10091 / 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
RfactorNum. reflection% reflectionSelection details
Rfree0.275 --RANDOM
Rwork0.2119 ---
obs0.2075 13894 94.8 %-
all-15686 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1975) 201-228
Displacement parametersBiso mean: 54.404 Å2
Refine analyzeLuzzati coordinate error obs: 0.263 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2696
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 0 0 252 2696
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.02
X-RAY DIFFRACTIONs_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.051
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.019
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.083
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs
2.15-2.250.292X-RAY DIFFRACTION1712
2.25-2.350.278X-RAY DIFFRACTION1439
2.35-2.480.257X-RAY DIFFRACTION1640
2.48-2.660.217X-RAY DIFFRACTION1520
2.66-2.860.2X-RAY DIFFRACTION1619
2.86-3.110.191X-RAY DIFFRACTION1488
3.11-3.50.197X-RAY DIFFRACTION1618
3.5-4.130.18X-RAY DIFFRACTION1559
4.13-6.580.188X-RAY DIFFRACTION1529
6.58-300.288X-RAY DIFFRACTION563

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