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- PDB-2qvw: Structure of Giardia Dicer refined against twinned data -

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Basic information

Entry
Database: PDB / ID: 2qvw
TitleStructure of Giardia Dicer refined against twinned data
ComponentsGLP_546_48378_50642
KeywordsHYDROLASE / Dicer / RNAi / pseudo-merohedral twin
Function / homology
Function and homology information


deoxyribonuclease I activity / ribonuclease III activity / pre-miRNA processing / siRNA processing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RISC complex / nucleotide binding / RNA binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Rna Polymerase Sigma Factor; Chain: A - #150 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1440 / Giardia dicer, N-terminal / Giardia Dicer N-terminal domain / Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / paz domain / paz domain / Ribonuclease III domain / Rna Polymerase Sigma Factor; Chain: A ...Rna Polymerase Sigma Factor; Chain: A - #150 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1440 / Giardia dicer, N-terminal / Giardia Dicer N-terminal domain / Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / paz domain / paz domain / Ribonuclease III domain / Rna Polymerase Sigma Factor; Chain: A / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / Ribonuclease III, endonuclease domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Beta Complex / Helix non-globular / Special / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Endoribonuclease Dicer-like / :
Similarity search - Component
Biological speciesGiardia intestinalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsDoudna, J.A. / MacRae, I.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer
Authors: Macrae, I.J. / Doudna, J.A.
History
DepositionAug 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Aug 30, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLP_546_48378_50642
B: GLP_546_48378_50642
C: GLP_546_48378_50642
D: GLP_546_48378_50642
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,90343
Polymers330,7604
Non-polymers2,14339
Water00
1
A: GLP_546_48378_50642
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,34913
Polymers82,6901
Non-polymers65912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GLP_546_48378_50642
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,18510
Polymers82,6901
Non-polymers4949
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GLP_546_48378_50642
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,18510
Polymers82,6901
Non-polymers4949
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GLP_546_48378_50642
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,18510
Polymers82,6901
Non-polymers4949
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.409, 173.490, 155.453
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit is a monomer. There are four copies in the asymmetric unit.

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Components

#1: Protein
GLP_546_48378_50642


Mass: 82690.070 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia intestinalis (eukaryote) / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q7R2M2, UniProt: A8BQJ3*PLUS, ribonuclease III
#2: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: Mn

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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: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% PEG 400, 0.1M NaCl, 0.1M MgCl2, 0.1M MES, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: l,-k,h / Fraction: 0.5
ReflectionResolution: 3→50 Å / Num. all: 84015 / Num. obs: 82755 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Biso Wilson estimate: 68.7 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 20.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 4.21 / Num. unique all: 8238 / Rsym value: 0.371 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementStarting model: PDB entry 2FFL

2ffl


Resolution: 3→50 Å / σ(F): 1517
Details: The authors state that the structure is the same as the previously deposited Dicer structure (PDB entry 2FFL) except the new model has been refined against higher resolution, twinned data.
RfactorNum. reflection% reflection
Rfree0.263 3938 4.6 %
Rwork0.221 --
obs-81205 95.9 %
Solvent computationBsol: 21.105 Å2
Displacement parametersBiso mean: 39.525 Å2
Baniso -1Baniso -2Baniso -3
1--1.872 Å20 Å20 Å2
2--4.251 Å20 Å2
3----2.38 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22333 0 39 0 22372
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.207
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.param

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