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- PDB-2ffl: Crystal Structure of Dicer from Giardia intestinalis -

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Basic information

Entry
Database: PDB / ID: 2ffl
TitleCrystal Structure of Dicer from Giardia intestinalis
ComponentsDicer
KeywordsTRANSLATION / HYDROLASE / RNA interference / RNAi / PAZ domain
Function / homology
Function and homology information


ribonuclease III activity / regulatory ncRNA-mediated gene silencing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA processing / nucleotide binding / RNA binding / metal ion binding
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 / PAZ domain profile. / 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 / MAD / Resolution: 3.33 Å
AuthorsDoudna, J.A. / MacRae, I.J. / Adams, P.D.
CitationJournal: Science / Year: 2006
Title: Structural Basis of Double-Stranded RNA Processing by Dicer
Authors: MacRae, I.J. / Zhou, K. / Li, F. / Repic, A. / Brooks, A.N. / Cande, W.Z. / Adams, P.D. / Doudna, J.A.
History
DepositionDec 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 14, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)332,90343
Polymers330,7604
Non-polymers2,14339
Water97354
1
A: Dicer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,34913
Polymers82,6901
Non-polymers65912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dicer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,18510
Polymers82,6901
Non-polymers4949
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dicer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,23911
Polymers82,6901
Non-polymers54910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dicer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1309
Polymers82,6901
Non-polymers4408
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
A: Dicer
hetero molecules

B: Dicer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,53423
Polymers165,3802
Non-polymers1,15421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+1/2,y+1/2,-z1
Buried area4050 Å2
ΔGint-92 kcal/mol
Surface area62720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.515, 174.101, 152.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYAA-1 - 7541 - 756
2ALAALABB0 - 7542 - 756
3ALAALAC - BC - B0 - 7542 - 756
4ALAALAD - BD - B0 - 7542 - 756

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Components

#1: Protein
Dicer / / E.C.3.1.26.3 / ribonuclease III


Mass: 82690.070 Da / Num. of mol.: 4 / Mutation: N-terminal GA residues
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia intestinalis (eukaryote) / Strain: Portland-1 / Plasmid: pFastBac HTa / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf-9
References: GenBank: 71078474, 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% PEG 400, 0.1M NaCl, 0.1M MnCl2, 0.1M MES, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 26, 2005
RadiationMonochromator: Double crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection

D res low: 50 Å

Redundancy (%)IDNumberRmerge(I) obsΧ2D res high (Å)% possible obs
3.61787560.1421.0413.899.9
3.42352820.1741.006498.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
8.185099.410.0440.9743.6
6.498.1899.910.0841.0413.6
5.676.4999.910.1511.0253.7
5.165.6710010.1621.0363.6
4.795.1610010.1611.0563.6
4.54.7910010.1751.0623.5
4.284.599.910.2081.0283.5
4.094.2899.910.2621.0383.6
3.944.0999.910.3521.0773.4
3.83.9499.910.471.0743.6
8.65097.420.0421.0053.3
6.848.698.420.0880.9263.5
5.976.8499.320.191.0243.5
5.435.9799.620.2430.9723.5
5.045.4399.620.2321.0273.5
4.745.0499.720.2481.0143.5
4.54.7499.620.2691.0673.4
4.314.599.120.3210.9663.4
4.144.319920.3911.0083.4
44.1497.920.5031.0633.3
ReflectionResolution: 3.33→50 Å / Num. all: 62442 / Num. obs: 60717 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.114 / Χ2: 1.042
Reflection shellResolution: 3.33→3.42 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.426 / Num. unique all: 5983 / Χ2: 1.075 / % possible all: 99.3

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 3.07 Å / D res low: 49.69 Å / FOM : 0.16 / FOM acentric: 0.174 / FOM centric: 0 / Reflection: 75847 / Reflection acentric: 69887 / Reflection centric: 5960
Phasing MAD set

R cullis centric: 1 / Highest resolution: 3.07 Å / Lowest resolution: 49.69 Å / Power acentric: 0 / Power centric: 0

IDR cullis acentricLoc acentricLoc centricReflection acentricReflection centric
11.91.71.3698875960
21145.3200.6478924598
31165.3220318043278
Phasing MAD set shell

Power acentric: 0 / Power centric: 0

IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricReflection acentricReflection centric
117.14-49.691.9918.54.2327166
110.35-17.141.5318.25.51343330
17.42-10.351.3815.64.23092505
15.78-7.422.5714.91.75549670
14.73-5.782.112.91.18761863
14.01-4.731.8711.40.6126901032
13.48-4.014.7310.60.1173351166
13.07-3.48110.40.3207901228
217.14-49.6911186.4282.5327149
210.35-17.1411183.4255.51343322
27.42-10.3511171.2245.13092499
25.78-7.4211131.4167.75548665
24.73-5.7811147.9198.28757860
24.01-4.7311158.8203.9126841029
23.48-4.0111129.1171.1161411074
23.07-3.48000000
317.14-49.6911188.5277.6326144
310.35-17.1411194.7261.51339290
37.42-10.3511177.5246.73089449
35.78-7.4211139.8174.35549621
34.73-5.7811159.3210.88760833
34.01-4.7311174224.112556930
33.48-4.0111168208.818511
33.07-3.48000000
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1ANO101.868-0.043-0.232-0.9620
2ANO99.361-0.549-0.227-0.9430
3ANO128.896-0.694-0.025-0.3060
4ANO96.294-0.41-0.239-0.9120
5ANO125.743-0.212-0.011-0.2970
6ANO115.314-0.41-0.245-0.0570
7ANO104.514-0.796-0.008-0.1560
8ANO144.79-0.823-0.087-0.1170
9ANO106.65-0.655-0.014-0.1710
10ANO153.579-0.373-0.166-0.0910
11ANO83.474-0.79-0.082-0.130
12ANO103.943-0.448-0.231-0.9040
13ANO101.46-0.226-0.019-0.2710
14ANO118.164-0.192-0.001-0.1880
15ANO92.982-0.65-0.02-0.2050
16ANO98.448-0.522-0.22-0.9520
17ANO114.782-0.942-0.245-0.9310
18ANO62.223-0.603-0.083-0.9390
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
17.14-49.690.3160.4770493327166
10.35-17.140.420.523016731343330
7.42-10.350.4220.491035973092505
5.78-7.420.3720.417062195549670
4.73-5.780.3030.333096248761863
4.01-4.730.1940.21013722126901032
3.48-4.010.10.107018501173351166
3.07-3.4800022018207901228
Phasing dmFOM : 0.64 / FOM acentric: 0.64 / FOM centric: 0.66 / Reflection: 75847 / Reflection acentric: 69887 / Reflection centric: 5960
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.8-49.6830.940.950.9334642768696
5.5-8.80.860.870.831028791361151
4.4-5.50.830.840.7812813117291084
3.9-4.40.760.760.71284311923920
3.3-3.90.550.550.4922701213511350
3.1-3.30.260.260.221373912980759

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Processing

Software
NameVersionClassification
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMAC5.2refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 3.33→20 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.863 / SU B: 56.07 / SU ML: 0.435 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.568 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27452 3117 5 %RANDOM
Rwork0.24294 ---
all0.24451 62442 --
obs0.24451 62442 99.48 %-
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: 41.284 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20 Å2
2---0.04 Å20 Å2
3---1.48 Å2
Refinement stepCycle: LAST / Resolution: 3.33→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22333 0 39 54 22426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02222846
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.97731081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.96552863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83422.832904
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.887153697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.03615156
X-RAY DIFFRACTIONr_chiral_restr0.0710.23622
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217053
X-RAY DIFFRACTIONr_nbd_refined0.2260.210503
X-RAY DIFFRACTIONr_nbtor_refined0.3060.215961
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2577
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.2146
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3780.27
X-RAY DIFFRACTIONr_mcbond_it0.7061.514719
X-RAY DIFFRACTIONr_mcangle_it1.132223292
X-RAY DIFFRACTIONr_scbond_it1.05739012
X-RAY DIFFRACTIONr_scangle_it1.8194.57789
Refine LS restraints NCS

Ens-ID: 1 / Number: 5485 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.380.25
2BTIGHT POSITIONAL0.410.25
3CTIGHT POSITIONAL0.280.25
4DTIGHT POSITIONAL0.390.25
1ATIGHT THERMAL0.462.5
2BTIGHT THERMAL0.422.5
3CTIGHT THERMAL0.412.5
4DTIGHT THERMAL0.392.5
LS refinement shellResolution: 3.33→3.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 230 -
Rwork0.272 4231 -
obs-4461 99.38 %
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)
11.02450.04470.67110.26790.05560.5450.0152-0.0477-0.01640.0949-0.01850.06270.04080.00470.0033-0.2375-0.01610.0452-0.193-0.0008-0.162113.307962.007816.2874
21.6929-0.6161-0.80840.55030.37950.95090.0079-0.0113-0.0567-0.01120.01220.06040.05210.0164-0.0202-0.2372-0.0404-0.0015-0.23320.0226-0.128710.715825.5931-14.2775
30.86860.2865-0.78640.4834-0.48451.34060.05290.0410.0264-0.0226-0.0028-0.0029-0.13060.1575-0.05010.1961-0.09280.15540.0984-0.0029-0.003753.1348104.7967-48.4347
40.94810.07650.59010.30040.23761.0333-0.05840.3302-0.1903-0.20190.03820.0702-0.03030.25240.02030.0163-0.02620.0572-0.034-0.05480.016121.794768.4034-53.5682
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 135
2X-RAY DIFFRACTION1A136 - 250
3X-RAY DIFFRACTION1A251 - 267
4X-RAY DIFFRACTION1A268 - 754
5X-RAY DIFFRACTION2B0 - 135
6X-RAY DIFFRACTION2B136 - 250
7X-RAY DIFFRACTION2B251 - 267
8X-RAY DIFFRACTION2B268 - 754
9X-RAY DIFFRACTION3C0 - 135
10X-RAY DIFFRACTION3C136 - 250
11X-RAY DIFFRACTION3C251 - 267
12X-RAY DIFFRACTION3C268 - 754
13X-RAY DIFFRACTION4D0 - 135
14X-RAY DIFFRACTION4D136 - 250
15X-RAY DIFFRACTION4D251 - 267
16X-RAY DIFFRACTION4D268 - 754

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