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

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Basic information

Entry
Database: PDB / ID: 5ixc
TitleHuman GIVD cytosolic phospholipase A2 in complex with Methyl gamma-Linolenyl Fluorophosphonate
ComponentsCytosolic phospholipase A2 delta
KeywordsHYDROLASE/HYDROLASE inhibitor / Inhibitor / Signal Transduction / Phospholipase / alpha/beta hydrolase / Calcium binding / C2 domain / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


phosphatidylglycerol acyl-chain remodeling / phosphatidylinositol acyl-chain remodeling / glycerophospholipid catabolic process / Hydrolysis of LPC / Acyl chain remodelling of PG / phospholipase A1 activity / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE ...phosphatidylglycerol acyl-chain remodeling / phosphatidylinositol acyl-chain remodeling / glycerophospholipid catabolic process / Hydrolysis of LPC / Acyl chain remodelling of PG / phospholipase A1 activity / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / calcium-dependent phospholipid binding / calcium-dependent phospholipase A2 activity / phospholipase A2 / 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 / Acyl transferase/acyl hydrolase/lysophospholipase / C2 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 / Acyl transferase/acyl hydrolase/lysophospholipase / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Chem-7FA / : / Cytosolic phospholipase A2 delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,40110
Polymers182,8892
Non-polymers1,5138
Water1,27971
1
A: Cytosolic phospholipase A2 delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2015
Polymers91,4441
Non-polymers7564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytosolic phospholipase A2 delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2015
Polymers91,4441
Non-polymers7564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.567, 111.379, 157.645
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 15 - 808 / Label seq-ID: 19 - 812

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

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Components

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


Mass: 91444.305 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C19H34FO2P
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ba
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES (pH 6.0-6.2), 50 mM sodium acetate, and 10-14% (v/v) PEG20K
PH range: 6.0-6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.997648 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997648 Å / Relative weight: 1
ReflectionResolution: 2.65→90.97 Å / Num. obs: 52014 / % possible obs: 100 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 20
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IZR

5izr


Resolution: 2.65→90.97 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.928 / SU B: 12.931 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 0.905 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25068 2647 5.1 %RANDOM
Rwork0.23659 ---
obs0.23732 49299 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.842 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0 Å2-0 Å2
2--3.13 Å2-0 Å2
3----3.4 Å2
Refinement stepCycle: LAST / Resolution: 2.65→90.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10840 0 50 71 10961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911129
X-RAY DIFFRACTIONr_bond_other_d0.0050.0210614
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9815079
X-RAY DIFFRACTIONr_angle_other_deg0.91324441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32751348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53923.762521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.119151883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1921584
X-RAY DIFFRACTIONr_chiral_restr0.0730.21670
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112451
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022549
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_it3.4056.3765440
X-RAY DIFFRACTIONr_mcbond_other3.4056.3775441
X-RAY DIFFRACTIONr_mcangle_it5.6249.5446772
X-RAY DIFFRACTIONr_mcangle_other5.6249.5436773
X-RAY DIFFRACTIONr_scbond_it3.5546.7855689
X-RAY DIFFRACTIONr_scbond_other3.5546.7865690
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.94410.0188308
X-RAY DIFFRACTIONr_long_range_B_refined9.60850.07112001
X-RAY DIFFRACTIONr_long_range_B_other9.60650.07511998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 41535 / 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: 2.652→2.721 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 190 -
Rwork0.358 3567 -
obs--98.92 %

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