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- PDB-3elo: Crystal Structure of Human Pancreatic Prophospholipase A2 -

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Basic information

Entry
Database: PDB / ID: 3elo
TitleCrystal Structure of Human Pancreatic Prophospholipase A2
ComponentsPhospholipase A2
KeywordsHYDROLASE / Human Pancreatic Prophospholipase A2 / Trimeric / Lipid degradation / Metal-binding / Secreted
Function / homology
Function and homology information


: / Acyl chain remodelling of PG / regulation of D-glucose import / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / positive regulation of podocyte apoptotic process / Synthesis of PA / phosphatidylglycerol metabolic process ...: / Acyl chain remodelling of PG / regulation of D-glucose import / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / positive regulation of podocyte apoptotic process / Synthesis of PA / phosphatidylglycerol metabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / Developmental Lineage of Pancreatic Acinar Cells / leukotriene biosynthetic process / bile acid binding / phospholipase A2 / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity / arachidonate secretion / positive regulation of calcium ion transport into cytosol / positive regulation of MAP kinase activity / lipid catabolic process / neutrophil chemotaxis / actin filament organization / innate immune response in mucosa / positive regulation of interleukin-8 production / positive regulation of protein secretion / phospholipid binding / positive regulation of immune response / cellular response to insulin stimulus / positive regulation of fibroblast proliferation / fatty acid biosynthetic process / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / intracellular signal transduction / signaling receptor binding / positive regulation of cell population proliferation / calcium ion binding / cell surface / signal transduction / positive 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsXu, W. / Yi, L. / Feng, Y. / Chen, L. / Liu, J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural insight into the activation mechanism of human pancreatic prophospholipase A2
Authors: Xu, W. / Yi, L. / Feng, Y. / Chen, L. / Liu, J.
History
DepositionSep 22, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9672
Polymers14,8711
Non-polymers961
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phospholipase A2
hetero molecules

A: Phospholipase A2
hetero molecules

A: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9016
Polymers44,6123
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area5670 Å2
ΔGint-71 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.549, 56.549, 60.631
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-127-

SO4

21A-127-

SO4

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Components

#1: Protein Phospholipase A2 / Phosphatidylcholine 2-acylhydrolase / Group IB phospholipase A2


Mass: 14870.794 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G1B / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P04054, phospholipase A2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1.88 Å3/Da / Density % sol: 34.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.4
Details: 0.1M Tris, 0.2M lithium sulfate, 33% PEG 4000, pH 8.4, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCED ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Dec 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→18.683 Å / Num. obs: 16060 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 7.879
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.55-1.633.80.5131.4874923230.513100
1.63-1.734.10.3862907922190.386100
1.73-1.854.20.3511.7879220790.351100
1.85-24.90.1741.6938219310.174100
2-2.195.20.1076.9932117780.107100
2.19-2.455.70.0749.9931116260.074100
2.45-2.836.50.05613.1927714330.056100
2.83-3.4770.03818843411990.038100
3.47-4.98.50.0321.880159470.03100
4.9-19.057.50.02724.839495250.02798.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
MOLREPphasing
REFMAC5.5.0044refinement
PDB_EXTRACT3.006data extraction
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→18.68 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 3.326 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.183 810 5 %RANDOM
Rwork0.145 ---
obs0.147 16042 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 36.78 Å2 / Biso mean: 8.896 Å2 / Biso min: 2.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.55→18.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1033 0 5 164 1202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221093
X-RAY DIFFRACTIONr_bond_other_d0.0020.02756
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9551486
X-RAY DIFFRACTIONr_angle_other_deg0.9363.0151835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7895140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.67625.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99815185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.309153
X-RAY DIFFRACTIONr_chiral_restr0.0870.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211235
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02215
X-RAY DIFFRACTIONr_mcbond_it0.5241.5678
X-RAY DIFFRACTIONr_mcbond_other0.1511.5272
X-RAY DIFFRACTIONr_mcangle_it0.91521093
X-RAY DIFFRACTIONr_scbond_it1.6113415
X-RAY DIFFRACTIONr_scangle_it2.5714.5390
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 63 -
Rwork0.243 1111 -
all-1174 -
obs--100 %
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)
16.92970.08011.97947.198-5.19755.3118-0.09481.1781-0.4957-0.6798-0.1368-0.60380.62160.51930.23150.09070.01010.05330.2091-0.07650.0889-7.7451-28.8047-6.1866
20.6998-0.5508-1.28681.23570.88992.3938-0.007-0.07650.01540.06870.0183-0.09120.02030.1337-0.01120.0413-0.004-0.00070.0603-0.00320.0479-7.1289-25.22485.8264
31.60960.82330.02141.65192.47935.032-0.0352-0.1563-0.16360.1973-0.05-0.01730.41020.05630.08520.04940.01720.02180.04060.01450.0477-13.3385-31.18798.1476
40.6379-0.24261.18531.0738-0.48423.9264-0.00780.0835-0.0196-0.00910.0036-0.0114-0.03710.0470.00420.032-0.00640.00640.0475-0.00330.0477-18.4974-30.726-6.9702
51.60690.8899-0.19641.50010.33240.7535-0.02240.11930.0765-0.06530.02480.0607-0.0381-0.0706-0.00240.03840.0132-0.00660.06920.00130.0482-19.5381-23.37-4.584
611.1237-1.0881-0.93973.0880.19064.6658-0.0440.62680.2746-0.34280.13430.0877-0.2595-0.1192-0.09040.0811-0.00550.0120.0650.02220.0682-5.9748-12.7195-10.136
70.23760.63560.18534.1104-1.73572.2133-0.0270.0112-0.0244-0.0995-0.0099-0.1327-0.00790.03890.0370.02070.01350.02340.04360.00470.0604-0.9074-21.8424-5.9617
82.9690.2947-1.9551.9497-0.40435.08890.0309-0.00360.08290.0107-0.0643-0.0908-0.43210.09020.03340.06010.0053-0.01120.0362-0.00370.0267-8.4008-14.4089.8012
92.53271.4304-0.52772.2199-0.44441.29420.0359-0.00120.11150.0131-0.0381-0.0232-0.07530.0230.00220.04940.0179-0.00040.0521-0.00460.0561-11.7229-15.86482.1135
103.322-1.797-1.30072.36712.32243.04060.0172-0.069-0.0510.0232-0.0086-0.02410.0814-0.0794-0.00860.0374-0.01530.0140.04890.00580.053-22.8784-34.64831.7245
111.9358-1.64252.1657.9472-5.54858.76610.15650.04-0.264-0.1998-0.09830.14310.48250.067-0.05820.04830.002-0.00420.0548-0.010.047-23.9169-37.1271-13.5962
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - 0
2X-RAY DIFFRACTION2A1 - 10
3X-RAY DIFFRACTION3A11 - 22
4X-RAY DIFFRACTION4A23 - 36
5X-RAY DIFFRACTION5A37 - 54
6X-RAY DIFFRACTION6A55 - 60
7X-RAY DIFFRACTION7A61 - 71
8X-RAY DIFFRACTION8A72 - 87
9X-RAY DIFFRACTION9A88 - 107
10X-RAY DIFFRACTION10A108 - 118
11X-RAY DIFFRACTION11A119 - 126

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