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- PDB-4gel: Crystal structure of Zucchini -

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Basic information

Entry
Database: PDB / ID: 4gel
TitleCrystal structure of Zucchini
ComponentsMitochondrial cardiolipin hydrolase
KeywordsHYDROLASE / piRNA / Phospholipase D / Nuclease
Function / homology
Function and homology information


Synthesis of PA / cardiolipin hydrolase activity / primary piRNA processing / oocyte karyosome formation / RNA endonuclease activity, producing 5'-phosphomonoesters / dorsal appendage formation / piRNA processing / cytoplasmic side of mitochondrial outer membrane / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / P granule ...Synthesis of PA / cardiolipin hydrolase activity / primary piRNA processing / oocyte karyosome formation / RNA endonuclease activity, producing 5'-phosphomonoesters / dorsal appendage formation / piRNA processing / cytoplasmic side of mitochondrial outer membrane / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / P granule / regulatory ncRNA-mediated gene silencing / oogenesis / lipid catabolic process / mitochondrion / identical protein binding
Similarity search - Function
Phospholipase D-like domain / PLD-like domain / Endonuclease Chain A / Endonuclease; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Mitochondrial cardiolipin hydrolase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.756 Å
AuthorsNishimasu, H. / Fukuhara, S. / Ishitani, R. / Nureki, O.
CitationJournal: Nature / Year: 2012
Title: Structure and function of Zucchini endoribonuclease in piRNA biogenesis
Authors: Nishimasu, H. / Ishizu, H. / Saito, K. / Fukuhara, S. / Kamatani, M.K. / Bonnefond, L. / Matsumoto, N. / Nishizawa, T. / Nakanaga, K. / Aoki, J. / Ishitani, R. / Siomi, H. / Siomi, M.C. / Nureki, O.
History
DepositionAug 2, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 8, 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 / 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.ptnr2_auth_asym_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.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_label_asym_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: Mitochondrial cardiolipin hydrolase
B: Mitochondrial cardiolipin hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,19811
Polymers49,6002
Non-polymers5989
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-3 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.994, 71.172, 56.318
Angle α, β, γ (deg.)90.000, 107.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mitochondrial cardiolipin hydrolase / Mitochondrial phospholipase homolog / MitoPLD / Protein zucchini


Mass: 24799.928 Da / Num. of mol.: 2 / Fragment: DmZuc, UNP residues 41-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: zuc, CG12314 / Plasmid: pCold-GST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: Q9VKD7, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.11 Å3/Da / Density % sol: 41.83 % / Mosaicity: 0.648 °
Crystal growMethod: vapor diffusion / Details: vapor diffusion

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorDate: May 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 39875 / % possible obs: 97.2 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.064 / Χ2: 1.202 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.783.70.33818350.47191.2
1.78-1.8140.32419390.485193.6
1.81-1.854.20.30618970.492194.8
1.85-1.894.40.27719540.549195.6
1.89-1.934.70.2619980.672195.7
1.93-1.974.90.22519120.628195.5
1.97-2.025.10.20319910.702196.3
2.02-2.075.40.18119820.778197.4
2.07-2.145.60.16719860.837197.2
2.14-2.25.70.13919860.893197.4
2.2-2.285.80.13619921.2197.1
2.28-2.386.20.11120141.051198.1
2.38-2.486.30.09920181.075198.7
2.48-2.616.40.09220171.146198.4
2.61-2.786.60.08120371.226199
2.78-2.996.90.06920291.337199
2.99-3.2970.06120591.705199.4
3.29-3.777.20.05420402.2199.5
3.77-4.757.40.04220852.041199.7
4.75-507.20.03921041.985199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GEN

4gen


Resolution: 1.756→42.812 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8615 / SU ML: 0.43 / σ(F): 1.47 / Phase error: 21.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 2013 5.05 %
Rwork0.1869 --
obs0.189 39874 96.56 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.592 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 81.82 Å2 / Biso mean: 28.7247 Å2 / Biso min: 14.15 Å2
Baniso -1Baniso -2Baniso -3
1-5.5946 Å2-0 Å2-5.1808 Å2
2---3.0082 Å2-0 Å2
3----2.5863 Å2
Refinement stepCycle: LAST / Resolution: 1.756→42.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3061 0 31 180 3272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083158
X-RAY DIFFRACTIONf_angle_d1.0914257
X-RAY DIFFRACTIONf_chiral_restr0.075497
X-RAY DIFFRACTIONf_plane_restr0.003530
X-RAY DIFFRACTIONf_dihedral_angle_d13.4311173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.756-1.80030.30311050.27162331243683
1.8003-1.84890.28951360.24082616275294
1.8489-1.90340.27021430.22622644278795
1.9034-1.96480.25281520.20832663281596
1.9648-2.0350.23831740.18612674284896
2.035-2.11650.21781260.17732734286098
2.1165-2.21280.20411450.16612720286597
2.2128-2.32950.22061560.17362713286998
2.3295-2.47540.22671430.17142745288898
2.4754-2.66650.23941590.17752750290999
2.6665-2.93480.24941570.1842775293299
2.9348-3.35930.21211420.18192790293299
3.3593-4.23180.22221250.175228362961100
4.2318-42.82450.22251500.195828703020100

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