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- PDB-3ism: Crystal structure of the EndoG/EndoGI complex: Mechanism of EndoG... -

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Basic information

Entry
Database: PDB / ID: 3ism
TitleCrystal structure of the EndoG/EndoGI complex: Mechanism of EndoG inhibition
Components
  • CG4930
  • CG8862
KeywordsHYDROLASE INHIBITOR/HYDROLASE / ENDONUCLEASE / ENDONUCLEASE INHIBITOR COMPLEX / METAL COMPLEX / Hydrolase / HYDROLASE INHIBITOR-HYDROLASE COMPLEX
Function / homology
Function and homology information


: / sperm mitochondrion organization / negative regulation of endoribonuclease activity / mitochondrion inheritance / hydrolase activity, acting on acid anhydrides / ribonuclease inhibitor activity / Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / Hydrolases; Acting on acid anhydrides / apoptotic DNA fragmentation / nuclease activity ...: / sperm mitochondrion organization / negative regulation of endoribonuclease activity / mitochondrion inheritance / hydrolase activity, acting on acid anhydrides / ribonuclease inhibitor activity / Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / Hydrolases; Acting on acid anhydrides / apoptotic DNA fragmentation / nuclease activity / single-stranded DNA endodeoxyribonuclease activity / positive regulation of Notch signaling pathway / spermatid development / ectopic germ cell programmed cell death / RNA endonuclease activity / DNA endonuclease activity / DNA-templated DNA replication / endonuclease activity / nucleic acid binding / mitochondrial inner membrane / mitochondrion / nucleus / metal ion binding
Similarity search - Function
Ku, C-terminal domain / DNA/RNA non-specific endonuclease, active site / DNA/RNA non-specific endonucleases active site. / Non-specific endonuclease / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Extracellular Endonuclease, subunit A ...Ku, C-terminal domain / DNA/RNA non-specific endonuclease, active site / DNA/RNA non-specific endonucleases active site. / Non-specific endonuclease / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Endonuclease / Endonuclease G inhibitor, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLoll, B. / Gebhardt, M. / Wahle, E. / Meinhart, A.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Crystal structure of the EndoG/EndoGI complex: mechanism of EndoG inhibition.
Authors: Loll, B. / Gebhardt, M. / Wahle, E. / Meinhart, A.
History
DepositionAug 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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.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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CG8862
B: CG8862
C: CG4930
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9886
Polymers101,8183
Non-polymers1713
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-14 kcal/mol
Surface area34800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.790, 109.150, 121.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CG8862 / Endonuclease G / EndoG / LD35517p


Mass: 30587.285 Da / Num. of mol.: 2 / Fragment: UNP residues 56-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG8862, Dmel_CG8862, EndoG / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q7JXB9
#2: Protein CG4930 / EndoGI / SD16985p


Mass: 40643.148 Da / Num. of mol.: 1 / Mutation: S2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: EndoGI, BG:DS07473.2, CG4930, Dmel_CG4930 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q9V3V9, EC: 3.6.1.3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20%(w/v)PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0075 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 4, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0075 Å / Relative weight: 1
ReflectionResolution: 2.2→43.23 Å / Num. all: 46364 / Num. obs: 46364 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 38 Å2 / Rsym value: 0.184 / Net I/σ(I): 14.8
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 5385 / Rsym value: 0.201 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O3B

2o3b


Resolution: 2.2→43.23 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 9.38 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22308 2412 5 %RANDOM
Rwork0.18444 ---
obs0.1864 45828 100 %-
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: 31.796 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2--0.37 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6299 0 10 328 6637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226611
X-RAY DIFFRACTIONr_angle_refined_deg1.151.9418994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8965818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42823.761351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.109151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6081551
X-RAY DIFFRACTIONr_chiral_restr0.0860.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025184
X-RAY DIFFRACTIONr_nbd_refined0.1790.32975
X-RAY DIFFRACTIONr_nbtor_refined0.3040.54472
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.5757
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.341
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.527
X-RAY DIFFRACTIONr_mcbond_it0.5331.54066
X-RAY DIFFRACTIONr_mcangle_it0.87826429
X-RAY DIFFRACTIONr_scbond_it1.37832900
X-RAY DIFFRACTIONr_scangle_it2.034.52542
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 175 -
Rwork0.201 3325 -
obs--100 %
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)
10.8226-0.1361-0.18892.4607-3.04493.92450.0391-0.1066-0.0711-0.1113-0.0320.48650.3028-0.0162-0.0071-0.1299-0.0248-0.02310.0335-0.0005-0.0347-36.657-37.58629.7591
20.89630.4545-0.2032.1689-0.67441.2657-0.0022-0.0461-0.04950.03730.03870.01140.1234-0.0621-0.0365-0.2317-0.0005-0.0163-0.1255-0.0144-0.1951-21.9544-37.883113.8288
312.16.94121.345811.65461.05119.16760.4222-0.8898-0.44570.8194-0.43510.47120.4476-0.58850.01290.0228-0.03160.04110.03310.0270.0151-13.439-8.638538.5849
41.75720.99930.19752.24230.18521.8696-0.08090.02780.091-0.13210.0726-0.1112-0.23460.12840.0083-0.05690.00180.0166-0.0918-0.0311-0.0467-6.33140.004623.1348
511.3852-10.08614.517526.3459-4.596414.7836-0.09480.32090.0997-0.533-0.3902-0.7682-0.54270.0560.4850.24860.00210.03130.1945-0.04710.152-8.3325-75.1461-0.3549
62.1324-2.42721.147712.55691.67592.98620.1757-0.1067-0.22580.21850.0229-0.21270.5108-0.228-0.19860.2398-0.0619-0.06350.07470.07390.1781-12.1249-79.306114.9819
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A67 - 90
2X-RAY DIFFRACTION1B65 - 90
3X-RAY DIFFRACTION2A91 - 311
4X-RAY DIFFRACTION2B91 - 311
5X-RAY DIFFRACTION3C21 - 48
6X-RAY DIFFRACTION4C49 - 174
7X-RAY DIFFRACTION5C219 - 274
8X-RAY DIFFRACTION6C275 - 354

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