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- PDB-5fis: Exonuclease domain-containing 1 (Exd1) in the Gd bound conformation -

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Basic information

Entry
Database: PDB / ID: 5fis
TitleExonuclease domain-containing 1 (Exd1) in the Gd bound conformation
Components(EXD1) x 2
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
GADOLINIUM ATOM / piRNA biogenesis protein EXD1
Similarity search - Component
Biological speciesBOMBYX MORI (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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 2, 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 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
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 / _pdbx_entry_details.has_protein_modification / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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.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 / _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

Downloads & links

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Assembly

Deposited unit
A: EXD1
B: EXD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7375
Polymers56,2652
Non-polymers4723
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-47.5 kcal/mol
Surface area23020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.860, 135.700, 51.460
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

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 75 - 315 / Label seq-ID: 3 - 243

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.99816, -0.00371, -0.06055), (-0.0077, -0.98229, 0.1872), (-0.06017, 0.18732, 0.98045)
Vector: 52.07223, 67.34358, -4.76237)

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Components

#1: Protein EXD1


Mass: 28118.447 Da / Num. of mol.: 1 / 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: Protein EXD1


Mass: 28146.463 Da / Num. of mol.: 1 / 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
#3: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Gd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 52.4 % / Description: OSCILLATION DATA WERE COLLECTED USING MXCUBEV2
Crystal growpH: 6
Details: 10% (W/V) PEG 2K, 200 MM KCL, 50 MM NA CACODYLATE (PH=6) 2 MM GDCL3,

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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: Oct 4, 2013 / 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: 1.6→50 Å / Num. obs: 143744 / % possible obs: 97.2 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.9 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
SHARPphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.6→50.01 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.257 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18245 3895 5.1 %RANDOM
Rwork0.1569 ---
obs0.15818 72884 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.586 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å20 Å2
2---0 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3909 0 3 411 4323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0194001
X-RAY DIFFRACTIONr_bond_other_d0.0110.023923
X-RAY DIFFRACTIONr_angle_refined_deg2.4731.965380
X-RAY DIFFRACTIONr_angle_other_deg1.70539065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8485486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38925.44193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49515786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.1851515
X-RAY DIFFRACTIONr_chiral_restr0.1510.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024453
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02898
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_it1.9931.9211932
X-RAY DIFFRACTIONr_mcbond_other1.9751.9191931
X-RAY DIFFRACTIONr_mcangle_it2.882.8732413
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0392.4542069
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

Ens-ID: 1 / Number: 30078 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 273 -
Rwork0.225 5249 -
obs--98.19 %
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)
10.25410.2654-0.08040.4633-0.07240.0338-0.0145-0.0003-0.0377-0.00670.0113-0.04510.00290.00790.00320.0038-0.00680.00060.02070.00040.018226.042824.51039.909
20.32180.33240.1250.66410.11820.0501-0.0221-0.00970.0514-0.0288-0.00060.0462-0.0074-0.00670.02280.0046-0.0045-0.00220.0097-0.00530.013225.44644.94577.9991
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 315
2X-RAY DIFFRACTION2B75 - 315

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