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- PDB-5fiq: Exonuclease domain-containing 1 (Exd1) in the native conformation -

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Basic information

Entry
Database: PDB / ID: 5fiq
TitleExonuclease domain-containing 1 (Exd1) in the native conformation
ComponentsEXD1
KeywordsHYDROLASE / EXONUCLEASE / PIRNA BIOGENESIS / DIMER / RNA BINDING
Function / homology
Function and homology information


PET complex / piRNA processing / P granule / regulatory ncRNA-mediated gene silencing / meiotic cell cycle / protein homodimerization activity / RNA binding
Similarity search - Function
3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
piRNA biogenesis protein EXD1
Similarity search - Component
Biological speciesBOMBYX MORI (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYang, Z. / Chen, K.M. / Pandey, R.R. / Homolka, D. / Reuter, M. / Rodino Janeiro, B.K. / Sachidanandam, R. / Fauvarque, M.O. / McCarthy, A.A. / Pillai, R.S.
CitationJournal: Mol.Cell / Year: 2016
Title: Piwi Slicing and Exd1 Drive Biogenesis of Nuclear Pirnas from Cytosolic Targets of the Mouse Pirna Pathway
Authors: Yang, Z. / Chen, K.M. / Pandey, R.R. / Homolka, D. / Reuter, M. / Rodino Janeiro, B.K. / Sachidanandam, R. / Fauvarque, M.O. / Mccarthy, A.A. / Pillai, R.S.
History
DepositionOct 1, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EXD1
C: EXD1
E: EXD1
G: EXD1
I: EXD1


Theoretical massNumber of molelcules
Total (without water)140,5125
Polymers140,5125
Non-polymers00
Water95553
1
A: EXD1

A: EXD1


Theoretical massNumber of molelcules
Total (without water)56,2052
Polymers56,2052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5290 Å2
ΔGint-32.1 kcal/mol
Surface area22810 Å2
MethodPISA
2
C: EXD1
E: EXD1


Theoretical massNumber of molelcules
Total (without water)56,2052
Polymers56,2052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-29.8 kcal/mol
Surface area22900 Å2
MethodPISA
3
G: EXD1
I: EXD1


Theoretical massNumber of molelcules
Total (without water)56,2052
Polymers56,2052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-29.3 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.540, 81.580, 154.750
Angle α, β, γ (deg.)90.00, 111.10, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14A
24I
15C
25E
16C
26G
17C
27I
18E
28G
19E
29I
110G
210I

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEAA75 - 3133 - 241
21ILEILECB75 - 3133 - 241
12ILEILEAA75 - 3133 - 241
22ILEILEEC75 - 3133 - 241
13ILEILEAA75 - 3133 - 241
23ILEILEGD75 - 3133 - 241
14ILEILEAA75 - 3133 - 241
24ILEILEIE75 - 3133 - 241
15ASPASPCB75 - 3143 - 242
25ASPASPEC75 - 3143 - 242
16ASPASPCB75 - 3143 - 242
26ASPASPGD75 - 3143 - 242
17ASPASPCB75 - 3143 - 242
27ASPASPIE75 - 3143 - 242
18ASPASPEC75 - 3143 - 242
28ASPASPGD75 - 3143 - 242
19ASPASPEC75 - 3143 - 242
29ASPASPIE75 - 3143 - 242
110ASPASPGD75 - 3143 - 242
210ASPASPIE75 - 3143 - 242

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

NCS oper:
IDCodeMatrixVector
1given(0.408, 0.884, -0.23), (-0.884, 0.32, -0.341), (-0.228, 0.342, 0.911)25.29546, -10.95703, -23.40071
2given(-0.405, -0.883, 0.236), (-0.885, 0.314, -0.344), (0.229, -0.349, -0.909)-81.69623, -10.76337, 167.43901
3given(-0.57, 0.549, -0.611), (-0.558, -0.805, -0.203), (-0.603, 0.226, 0.765)88.85638, -28.88748, -7.94666
4given(0.574, -0.542, 0.613), (-0.545, -0.812, -0.207), (0.61, -0.215, -0.762)-144.68066, -28.84359, 152.25386

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Components

#1: Protein
EXD1


Mass: 28102.447 Da / Num. of mol.: 5 / Fragment: EXONUCLEASE DOMAIN, RESIDUES 73-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOMBYX MORI (domestic silkworm) / Cell line: BMN4 / Organ: OVARIES / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: H9IUR0*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN SEQUENCE CORRESPONDS TO MRNA SEQUENCE: GENBANK ID AK383154

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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: 2.58 Å3/Da / Density % sol: 52.3 %
Description: OSCILLATION DATA WERE COLLECTED USING MXCUBEV2.0
Crystal growpH: 8.5
Details: 35% (W/V) 1,6-HEXANEDIOL, 50 MM TRIS-HCL PH 8.5, 5 MM MGSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2014 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 53690 / % possible obs: 96 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.6
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.3 / % possible all: 85.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FIS

5fis


Resolution: 2.4→50.01 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.93 / SU B: 26.969 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R: 0.489 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24717 2596 4.8 %RANDOM
Rwork0.221 ---
obs0.22226 51094 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.371 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.51 Å2
2---3.16 Å20 Å2
3---2.25 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9685 0 0 53 9738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0199855
X-RAY DIFFRACTIONr_bond_other_d0.010.029623
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.96213261
X-RAY DIFFRACTIONr_angle_other_deg1.569322224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50251197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26225.532470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.378151918
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1151535
X-RAY DIFFRACTIONr_chiral_restr0.1130.21489
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211019
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022192
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6592.0644803
X-RAY DIFFRACTIONr_mcbond_other1.6582.0634802
X-RAY DIFFRACTIONr_mcangle_it2.823.0865995
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1062.3425051
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A299240.06
12C299240.06
21A299620.06
22E299620.06
31A299660.07
32G299660.07
41A297840.07
42I297840.07
51C298520.07
52E298520.07
61C298540.07
62G298540.07
71C297460.08
72I297460.08
81E297620.07
82G297620.07
91E299120.07
92I299120.07
101G299540.06
102I299540.06
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 148 -
Rwork0.326 3315 -
obs--83.81 %
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)
11.30260.0292-0.56170.36340.1630.61830.01440.0502-0.0467-0.08330.0114-0.09270.08720.0377-0.02580.24680.01780.0970.75380.00260.0606-15.924-29.02462.979
20.7590.4436-0.80671.157-0.35711.1320.10550.02910.14190.0370.0816-0.0411-0.05470.1693-0.18710.2027-0.00740.1010.8386-0.03010.0847-20.536-12.62694.348
30.46390.2596-0.46210.9152-0.04681.3969-0.0795-0.1926-0.01280.21950.07650.01720.25820.03660.0030.30110.01850.08550.83040.02210.0348-34.453-27.405116.745
40.9143-0.2341-0.06860.5176-0.44172.60720.01950.02930.1729-0.14090.1107-0.1162-0.1444-0.2366-0.13020.2759-0.02720.13290.8245-0.00150.095417.044-41.432118.309
50.5389-0.2083-0.45480.53660.18042.7222-0.046-0.33940.14590.11910.0766-0.01590.34390.2468-0.03060.28150.03340.08620.9692-0.05250.076319.599-50.492147.005
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A73 - 314
2X-RAY DIFFRACTION2C75 - 314
3X-RAY DIFFRACTION3E75 - 314
4X-RAY DIFFRACTION4G75 - 314
5X-RAY DIFFRACTION5I75 - 314

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