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- PDB-1le6: CARBOXYLIC ESTER HYDROLASE, P 1 21 1 SPACE GROUP -

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Basic information

Entry
Database: PDB / ID: 1le6
TitleCARBOXYLIC ESTER HYDROLASE, P 1 21 1 SPACE GROUP
ComponentsGroup X Secretory Phospholipase A2
KeywordsHYDROLASE / Human Phosphatidylcholine 2-acylhydrolase GX / GX sPLA2 / sPLA2-X
Function / homology
Function and homology information


nuclear receptor-mediated signaling pathway / phosphatidylserine metabolic process / phosphatidylethanolamine metabolic process / lysophospholipid transport / phosphatidic acid metabolic process / platelet activating factor catabolic process / positive regulation of acrosome reaction / Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI ...nuclear receptor-mediated signaling pathway / phosphatidylserine metabolic process / phosphatidylethanolamine metabolic process / lysophospholipid transport / phosphatidic acid metabolic process / platelet activating factor catabolic process / positive regulation of acrosome reaction / Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / phospholipase activity / Acyl chain remodelling of PE / 1-alkyl-2-acetylglycerophosphocholine esterase activity / Synthesis of PA / production of molecular mediator involved in inflammatory response / negative regulation of cholesterol efflux / intestinal stem cell homeostasis / arachidonate metabolic process / phosphatidylglycerol metabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / positive regulation of prostaglandin secretion / positive regulation of arachidonate secretion / macrophage activation / positive regulation of lipid storage / phospholipase A2 / low-density lipoprotein particle remodeling / positive regulation of macrophage derived foam cell differentiation / phosphatidylcholine catabolic process / calcium-dependent phospholipase A2 activity / fertilization / prostaglandin biosynthetic process / signal transduction involved in regulation of gene expression / arachidonate secretion / hair follicle morphogenesis / erythrocyte maturation / regulation of macrophage activation / positive regulation of protein metabolic process / negative regulation of cytokine production involved in inflammatory response / acrosomal vesicle / axon guidance / cholesterol homeostasis / cellular response to leukemia inhibitory factor / phospholipid binding / negative regulation of inflammatory response / defense response to virus / lysosome / calcium ion binding / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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: 1.97 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,4089
Polymers40,9343
Non-polymers4756
Water8,197455
1
A: Group X Secretory Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6852
Polymers13,6451
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 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
3
C: Group X Secretory Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6852
Polymers13,6451
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.173, 62.134, 70.368
Angle α, β, γ (deg.)90.00, 99.35, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 3
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.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.7 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG3500, MPD, ETHYLENE GLYCOL, CALCIUM CHLORIDE, HEPES BUFFER, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.4
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: Sep 7, 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: 1.9→28.36 Å / Num. all: 34475 / Num. obs: 34412 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 26
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 3399 / % possible all: 99.6
Reflection
*PLUS
Num. obs: 34475 / Num. measured all: 337721 / Rmerge(I) obs: 0.063

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Processing

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

1pob


Resolution: 1.97→28.36 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 413862.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1484 4.9 %RANDOM
Rwork0.19 ---
all0.192 30938 --
obs0.192 30149 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.3513 Å2 / ksol: 0.342686 e/Å3
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å20 Å24.34 Å2
2--1.98 Å20 Å2
3---0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.97→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 3 479 3317
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shellResolution: 1.97→2.09 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 223 4.7 %
Rwork0.228 4489 -
obs-4712 92.8 %
Refinement
*PLUS
Lowest resolution: 6 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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