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- PDB-3rv1: Crystal structure of the N-terminal and RNase III domains of K. p... -

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Basic information

Entry
Database: PDB / ID: 3rv1
TitleCrystal structure of the N-terminal and RNase III domains of K. polysporus Dcr1 E224Q mutant
ComponentsK. polysporus Dcr1
KeywordsRNA BINDING PROTEIN / RNase III enzyme
Function / homology
Function and homology information


ribonuclease III / ribonuclease III activity / rRNA processing / RNA binding / identical protein binding
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #260 / : / : / Dicers, N-terminal domain / Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #260 / : / : / Dicers, N-terminal domain / Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesVanderwaltozyma polyspora (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.975 Å
AuthorsNakanishi, K. / Weinberg, D.E. / Bartel, D.P. / Patel, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: The inside-out mechanism of dicers from budding yeasts.
Authors: Weinberg, D.E. / Nakanishi, K. / Patel, D.J. / Bartel, D.P.
History
DepositionMay 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: K. polysporus Dcr1
B: K. polysporus Dcr1


Theoretical massNumber of molelcules
Total (without water)56,7812
Polymers56,7812
Non-polymers00
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11160 Å2
ΔGint-97 kcal/mol
Surface area22270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.907, 96.405, 101.449
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein K. polysporus Dcr1


Mass: 28390.271 Da / Num. of mol.: 2 / Fragment: UNP residues 15-260 / Mutation: E224Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vanderwaltozyma polyspora (fungus) / Strain: DSM 70294 / Gene: Kpol_455p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)rosetta2 / References: UniProt: A7TR32
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 200 mM L-proline, 10% PEG3350, 100 mM HEPES buffer pH 7.5, vapor diffusion, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 40348 / % possible obs: 97.9 %

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXdev_538refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.975→48.203 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8237 / SU ML: 0.26 / σ(F): 0.13 / Phase error: 24.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 2018 5.01 %
Rwork0.1944 38293 -
obs0.1965 40311 97.69 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.335 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 129.46 Å2 / Biso mean: 26.3359 Å2 / Biso min: 1.62 Å2
Baniso -1Baniso -2Baniso -3
1-6.8006 Å20 Å20 Å2
2--14.8073 Å2-0 Å2
3---2.7947 Å2
Refinement stepCycle: LAST / Resolution: 1.975→48.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3699 0 0 262 3961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073764
X-RAY DIFFRACTIONf_angle_d0.9475087
X-RAY DIFFRACTIONf_chiral_restr0.066579
X-RAY DIFFRACTIONf_plane_restr0.003647
X-RAY DIFFRACTIONf_dihedral_angle_d13.4791395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.975-2.04590.39571930.34953607380094
2.0459-2.12780.33812030.29453730393396
2.1278-2.22460.25641870.24253751393897
2.2246-2.34190.26782090.2043838404798
2.3419-2.48860.24121940.19413804399898
2.4886-2.68080.25812010.19193835403698
2.6808-2.95050.23642060.17873850405699
2.9505-3.37730.20792070.17283850405798
3.3773-4.25470.19142030.1573944414799
4.2547-48.21680.20492150.17114084429999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.04710.02660.04060.12660.01480.1453-0.0395-0.0275-0.06560.04190.04830.00240.0104-0.13710.09360.04850.0034-0.00420.062-0.09870.0957-37.75615.1184-11.5692
20.1524-0.0131-0.02030.05340.01610.0137-0.02080.2609-0.2133-0.04950.0006-0.04180.04060.1162-0.08450.03430.04260.01630.1511-0.16720.0691-14.0453-2.9411-25.0134
30.09760.0224-0.02060.02890.02050.0744-0.02840.1069-0.0114-0.009-00.0996-0.061-0.14250.0379-0.01620.0052-0.0510.1065-0.07460.0523-38.10148.5309-18.6774
40.04220.04950.0230.1112-0.0130.1898-0.00760.0484-0.07090.0317-0.0006-0.127-0.0270.1948-0.0451-0.1331-0.0891-0.05720.03-0.02050.0463-9.54554.4079-7.394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 15:105))A0
2X-RAY DIFFRACTION2chain 'A' and ((resseq 106:256))A0
3X-RAY DIFFRACTION3chain 'B' and ((resseq 15:105))B0
4X-RAY DIFFRACTION4chain 'B' and ((resseq 106:258))B0

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