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- PDB-3n3w: 2.2 Angstrom Resolution Crystal Structure of Nuclease Domain of R... -

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Basic information

Entry
Database: PDB / ID: 3n3w
Title2.2 Angstrom Resolution Crystal Structure of Nuclease Domain of Ribonuclase III (rnc) from Campylobacter jejuni
ComponentsRibonuclease III
KeywordsHYDROLASE / Nuclease Domain / Ribonuclase III / idp90862 / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


ribonuclease III / ribonuclease III activity / tRNA processing / mRNA processing / rRNA processing / rRNA 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 family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double-stranded RNA binding motif / 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 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 speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.205 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.2 Angstrom Resolution Crystal Structure of Nuclease Domain of Ribonuclase III (rnc) from Campylobacter jejuni
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)55,4902
Polymers55,4902
Non-polymers00
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-15 kcal/mol
Surface area14710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.099, 98.252, 118.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-307-

HOH

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Components

#1: Protein Ribonuclease III /


Mass: 27744.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: rnc / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D3FPA5, UniProt: Q9PM40*PLUS, ribonuclease III
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN USED FOR CRYSTALLIZATION CONTAINED AMINO-ACIDS AS GIVEN IN DBREF. THIS PROTEIN LIKELY ...THE PROTEIN USED FOR CRYSTALLIZATION CONTAINED AMINO-ACIDS AS GIVEN IN DBREF. THIS PROTEIN LIKELY DEGRADED TO A TRUNCATED SPECIES DURING THE CRYSTALLIZATION EXPERIMENT. THEREFORE, CALCULATED VM AND VS VALUES ARE BASED ON AN ESTIMATE WITH THE ASSUMPTION THAT RESIDUES -23 TO 150 ARE PRESENT.

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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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein solution: 7.6 mg/mL, 0.5M Sodium chloride, 0.01M Tris pH 8.3 Screen solution: Classics II (F7), 0.2M Ammonium sulfate, 0.1M BIS-TRIS pH 6.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, ...Details: Protein solution: 7.6 mg/mL, 0.5M Sodium chloride, 0.01M Tris pH 8.3 Screen solution: Classics II (F7), 0.2M Ammonium sulfate, 0.1M BIS-TRIS pH 6.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97965 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 14, 2010 / Details: Si{1,1,1}
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97965 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 18659 / Num. obs: 18659 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 16.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 3.3 / Num. unique all: 929 / % possible all: 99.1

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A11

2a11


Resolution: 2.205→29.6 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.388 / SU ML: 0.088 / Isotropic thermal model: Individually refined / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23371 952 5.1 %RANDOM
Rwork0.17641 ---
all0.17922 17681 --
obs0.17922 17681 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.785 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å2-0 Å20 Å2
2--2.81 Å2-0 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.205→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 0 189 2490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222409
X-RAY DIFFRACTIONr_bond_other_d0.0010.021658
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.9773240
X-RAY DIFFRACTIONr_angle_other_deg0.84734085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.525303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36325.789114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02615470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.328157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022688
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02467
X-RAY DIFFRACTIONr_mcbond_it1.1871.51483
X-RAY DIFFRACTIONr_mcbond_other0.2981.5606
X-RAY DIFFRACTIONr_mcangle_it2.16322370
X-RAY DIFFRACTIONr_scbond_it3.2763926
X-RAY DIFFRACTIONr_scangle_it5.3114.5870
LS refinement shellResolution: 2.205→2.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 62 -
Rwork0.208 1283 -
obs-1283 98.97 %

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