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- PDB-4aup: Tuber borchii Phospholipase A2 -

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Basic information

Entry
Database: PDB / ID: 4aup
TitleTuber borchii Phospholipase A2
ComponentsPHOSPHOLIPASE A2 GROUP XIII
KeywordsHYDROLASE
Function / homology
Function and homology information


phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process
Similarity search - Function
Phospholipase A2, prokaryotic/fungal / Prokaryotic phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / THIOCYANATE ION / Phospholipase A2 group XIII
Similarity search - Component
Biological speciesTUBER BORCHII (whitish truffle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å
AuthorsCavazzini, D. / Meschi, F. / Corsini, R. / Bolchi, A. / Rossi, G.-L. / Einsle, O. / Ottonello, S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Autoproteolytic Activation of a Symbiosis-Regulated Truffle Phospholipase A2
Authors: Cavazzini, D. / Meschi, F. / Corsini, R. / Bolchi, A. / Rossi, G.-L. / Einsle, O. / Ottonello, S.
History
DepositionMay 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / 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 / 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 / _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: PHOSPHOLIPASE A2 GROUP XIII
B: PHOSPHOLIPASE A2 GROUP XIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6045
Polymers28,4282
Non-polymers1763
Water3,657203
1
A: PHOSPHOLIPASE A2 GROUP XIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2732
Polymers14,2141
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHOSPHOLIPASE A2 GROUP XIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3313
Polymers14,2141
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.498, 66.837, 117.384
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 PHOSPHOLIPASE A2 GROUP XIII


Mass: 14213.929 Da / Num. of mol.: 2 / Fragment: ACTIVE FORM, RESIDUES 89-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TUBER BORCHII (whitish truffle) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL / References: UniProt: Q9P4F6
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSTRUCTURE REPRESENTS AN AUTOPROTEOLYTICALLY PROCESSED FRAGMENT OF THE ENTIRE SEQUENCE. THE FIRST 91 ...STRUCTURE REPRESENTS AN AUTOPROTEOLYTICALLY PROCESSED FRAGMENT OF THE ENTIRE SEQUENCE. THE FIRST 91 RESIDUES OF THE FULL SEQUENCE ARE CLEAVED OFF. GENBANK ACCESSION NUMBER AAF80454.1

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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: 2.43 Å3/Da / Density % sol: 49.3 % / Description: NONE
Crystal growpH: 7.5
Details: 2.0 M AMMONIUM SULPHATE, 0.1 M HEPES, PH 7.5 2% PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 22164 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.85 / % possible all: 92.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.9→19.41 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 8.929 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27348 1112 5.1 %RANDOM
Rwork0.20961 ---
obs0.21279 20711 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.408 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å20 Å20 Å2
2---0.03 Å20 Å2
3----2.25 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 11 203 2198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022048
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.9392758
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6895241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06322.778108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50815344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.681520
X-RAY DIFFRACTIONr_chiral_restr0.150.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211614
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 61 -
Rwork0.331 1308 -
obs--94.22 %
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)
10.4260.3164-1.18210.404-1.29894.330.1153-0.1272-0.0216-0.0046-0.08760.0241-0.08630.3513-0.02770.0846-0.0244-0.00410.06370.01580.049411.186839.343311.2937
20.09080.0611-0.39581.1645-0.56831.81440.0231-0.0142-0.00020.08260.01160.061-0.11750.0653-0.03460.0154-0.00620.01360.0555-0.00020.0626-2.055134.84939.4503
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A94 - 211
2X-RAY DIFFRACTION2B94 - 211

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