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- PDB-5izr: Human GIVD cytosolic phospholipase A2 in complex with Methyl gamm... -

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Basic information

Entry
Database: PDB / ID: 5izr
TitleHuman GIVD cytosolic phospholipase A2 in complex with Methyl gamma-Linolenyl Fluorophosphonate inhibitor and Terbium Chloride
ComponentsCytosolic phospholipase A2 delta
KeywordsHYDROLASE/HYDROLASE inhibitor / Signal Transduction / phospholipase / inhibitor / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


phosphatidylglycerol acyl-chain remodeling / phosphatidylinositol acyl-chain remodeling / Hydrolysis of LPC / glycerophospholipid catabolic process / Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / phospholipase A1 activity ...phosphatidylglycerol acyl-chain remodeling / phosphatidylinositol acyl-chain remodeling / Hydrolysis of LPC / glycerophospholipid catabolic process / Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / phospholipase A1 activity / Synthesis of PA / calcium-dependent phospholipid binding / phospholipase A2 / calcium-dependent phospholipase A2 activity / fatty acid metabolic process / calcium ion binding / membrane / cytosol
Similarity search - Function
Cytosolic phospholipases A2, C2-domain / Cytosolic phospholipases A2 C2-domain / Lysophospholipase, catalytic domain / Cytosolic phospholipase A2, C2 domain / Lysophospholipase catalytic domain / PLA2c domain profile. / Cytoplasmic phospholipase A2, catalytic subunit / Cytosolic phospholipase A2 catalytic domain / Cytosolic phospholipase A2 catalytic domain / Protein kinase C conserved region 2 (CalB) ...Cytosolic phospholipases A2, C2-domain / Cytosolic phospholipases A2 C2-domain / Lysophospholipase, catalytic domain / Cytosolic phospholipase A2, C2 domain / Lysophospholipase catalytic domain / PLA2c domain profile. / Cytoplasmic phospholipase A2, catalytic subunit / Cytosolic phospholipase A2 catalytic domain / Cytosolic phospholipase A2 catalytic domain / Protein kinase C conserved region 2 (CalB) / C2 domain / Acyl transferase/acyl hydrolase/lysophospholipase / C2 domain / C2 domain profile. / C2 domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7FA / TERBIUM(III) ION / Cytosolic phospholipase A2 delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.25 Å
AuthorsWang, H. / Klein, M.G.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structure of Human GIVD Cytosolic Phospholipase A2 Reveals Insights into Substrate Recognition.
Authors: Wang, H. / Klein, M.G. / Snell, G. / Lane, W. / Zou, H. / Levin, I. / Li, K. / Sang, B.C.
History
DepositionMar 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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 / _pdbx_struct_oper_list.symmetry_operation / _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.ptnr1_symmetry / _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_conn_type.id / _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: Cytosolic phospholipase A2 delta
B: Cytosolic phospholipase A2 delta
C: Cytosolic phospholipase A2 delta
D: Cytosolic phospholipase A2 delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)369,53923
Polymers365,7774
Non-polymers3,76219
Water21612
1
A: Cytosolic phospholipase A2 delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4246
Polymers91,4441
Non-polymers9805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytosolic phospholipase A2 delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4246
Polymers91,4441
Non-polymers9805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytosolic phospholipase A2 delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2665
Polymers91,4441
Non-polymers8214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytosolic phospholipase A2 delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4246
Polymers91,4441
Non-polymers9805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.824, 112.667, 159.200
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 15 - 807 / Label seq-ID: 19 - 811

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Cytosolic phospholipase A2 delta / cPLA2-delta / Phospholipase A2 group IVD


Mass: 91444.305 Da / Num. of mol.: 4 / Fragment: UNP residues 2-810
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G4D / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q86XP0, phospholipase A2
#2: Chemical
ChemComp-7FA / methyl (R)-(6Z,9Z,12Z)-octadeca-6,9,12-trien-1-ylphosphonofluoridate


Mass: 344.444 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H34FO2P
#3: Chemical
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Tb
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES (pH 6.0-6.2), 10-14% (v/v) PEG20K and 50 mM sodium acetate
PH range: 6.0-6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.65 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.65 Å / Relative weight: 1
ReflectionResolution: 3.25→159.2 Å / Num. obs: 56076 / % possible obs: 99.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 9.9
Reflection shellResolution: 3.25→3.34 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.25→159.2 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.887 / SU B: 33.21 / SU ML: 0.511 / Cross valid method: THROUGHOUT / ESU R Free: 0.56 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26654 2849 5.1 %RANDOM
Rwork0.22988 ---
obs0.23174 53210 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.699 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å20 Å2-0.1 Å2
2--10.17 Å2-0 Å2
3----7.6 Å2
Refinement stepCycle: LAST / Resolution: 3.25→159.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21254 0 103 12 21369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01921802
X-RAY DIFFRACTIONr_bond_other_d0.0030.0220724
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.97929514
X-RAY DIFFRACTIONr_angle_other_deg0.882347690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7152623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24123.8821033
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.843153678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.75315159
X-RAY DIFFRACTIONr_chiral_restr0.0760.23271
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02124343
X-RAY DIFFRACTIONr_gen_planes_other0.0030.025000
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_it4.4388.38610639
X-RAY DIFFRACTIONr_mcbond_other4.4388.38710640
X-RAY DIFFRACTIONr_mcangle_it7.34812.55413213
X-RAY DIFFRACTIONr_mcangle_other7.34812.55513214
X-RAY DIFFRACTIONr_scbond_it4.3338.82211163
X-RAY DIFFRACTIONr_scbond_other4.3338.82211164
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.34413.06516302
X-RAY DIFFRACTIONr_long_range_B_refined11.22165.50623381
X-RAY DIFFRACTIONr_long_range_B_other11.22165.50823382
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)
11A414480.05
12B414480.05
21A408570.05
22C408570.05
31A415990.04
32D415990.04
41B406150.06
42C406150.06
51B409950.05
52D409950.05
61C405900.05
62D405900.05
LS refinement shellResolution: 3.25→3.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 218 -
Rwork0.361 3866 -
obs--99.01 %

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