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- PDB-1le7: CARBOXYLIC ESTER HYDROLASE, C 2 2 21 space group -

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Basic information

Entry
Database: PDB / ID: 1le7
TitleCARBOXYLIC ESTER HYDROLASE, C 2 2 21 space group
ComponentsGroup X Secretory Phospholipase A2
KeywordsHYDROLASE / Human Phosphatidylcholine 2-acylhydrolase GX / GX sPLA2 / sPLA2-X
Function / homology
Function and homology information


phosphatidylserine metabolic process / lysophospholipid transport / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / production of molecular mediator involved in inflammatory response / platelet activating factor catabolic process / positive regulation of acrosome reaction / Acyl chain remodelling of PG / intestinal stem cell homeostasis / phospholipase activity ...phosphatidylserine metabolic process / lysophospholipid transport / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / production of molecular mediator involved in inflammatory response / platelet activating factor catabolic process / positive regulation of acrosome reaction / Acyl chain remodelling of PG / intestinal stem cell homeostasis / phospholipase activity / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / 1-alkyl-2-acetylglycerophosphocholine esterase activity / Synthesis of PA / negative regulation of cholesterol efflux / arachidonic acid metabolic process / phosphatidylglycerol metabolic process / calcium-dependent phospholipase A2 activity / phosphatidylcholine catabolic process / positive regulation of prostaglandin secretion / positive regulation of macrophage derived foam cell differentiation / positive regulation of lipid storage / phosphatidylcholine metabolic process / macrophage activation / positive regulation of arachidonic acid secretion / low-density lipoprotein particle remodeling / fertilization / phospholipase A2 / phospholipase A2 activity / prostaglandin biosynthetic process / regulation of macrophage activation / arachidonic acid secretion / hair follicle morphogenesis / erythrocyte maturation / negative regulation of cytokine production involved in inflammatory response / phospholipid metabolic process / positive regulation of protein metabolic process / cellular response to leukemia inhibitory factor / acrosomal vesicle / cholesterol homeostasis / axon guidance / phospholipid binding / negative regulation of DNA-binding transcription factor activity / negative regulation of inflammatory response / defense response to virus / lysosome / calcium ion binding / extracellular space / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Group 10 secretory phospholipase A2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsPan, Y.H. / Jain, M.K. / Bahnson, B.J.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of human group X secreted phospholipase A2. Electrostatically neutral interfacial surface targets zwitterionic membranes.
Authors: Pan, Y.H. / Yu, B.Z. / Singer, A.G. / Ghomashchi, F. / Lambeau, G. / Gelb, M.H. / Jain, M.K. / Bahnson, B.J.
History
DepositionApr 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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_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_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 375 SPECIAL POSITION THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS OF A SYMMETRY RELATED ... SPECIAL POSITION THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS OF A SYMMETRY RELATED ATOM AND ARE AT SPECIAL POSITIONS. ATOM RES CSSEQI HOH 212 LIES ON A SPECIAL POSITION. HOH 213 LIES ON A SPECIAL POSITION. HOH 214 LIES ON A SPECIAL POSITION.
Remark 600HETEROGEN In subunit A, HOH 1 is the N-terminal associated water; 5 and 12 are calcium coordinated ...HETEROGEN In subunit A, HOH 1 is the N-terminal associated water; 5 and 12 are calcium coordinated waters; 6 is the putative catalytic assisted water.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Group X Secretory Phospholipase A2
B: Group X Secretory Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9609
Polymers27,2892
Non-polymers6717
Water3,783210
1
A: Group X Secretory Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0395
Polymers13,6451
Non-polymers3954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Group X Secretory Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9214
Polymers13,6451
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.058, 145.098, 28.086
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-376-

HOH

21A-377-

HOH

31A-378-

HOH

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Components

#1: Protein Group X Secretory Phospholipase A2 / Phosphatidylcholine 2-acylhydrolase GX / GX sPLA2 / sPLA2-X


Mass: 13644.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2GX10 / Production host: Escherichia coli (E. coli) / References: UniProt: O15496, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG3500, MPD, ETHYLENE GLYCOL, MJ33, CALCIUM CHLORIDE, HEPES BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
210 mM1dropCaCl2
33 mMMJ331drop
410 mM1reservoirCaCl2
512 %PEG35001reservoir
610 %MPD1reservoir
72 %ethylene glycol1reservoir
80.2 MHEPES1reservoirpH7.4

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 27, 2001 / Details: MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→24.5 Å / Num. all: 19931 / Num. obs: 19092 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 21
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1489 / % possible all: 78
Reflection
*PLUS
Num. obs: 19931 / Num. measured all: 184444

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LE6

1le6


Resolution: 2.09→24.51 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 440075.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 711 4.9 %RANDOM
Rwork0.211 ---
all0.228 17540 --
obs0.214 14657 83.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.8117 Å2 / ksol: 0.319815 e/Å3
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.87 Å20 Å20 Å2
2---2.72 Å20 Å2
3----2.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.09→24.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 2 250 2142
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_mcangle_it1.622
X-RAY DIFFRACTIONc_scbond_it1.62
X-RAY DIFFRACTIONc_scangle_it2.42.5
LS refinement shellResolution: 2.09→2.22 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 88 5 %
Rwork0.236 1680 -
obs-1768 61.7 %
Refinement
*PLUS
Lowest resolution: 6 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.14
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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