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- PDB-1zm6: Crystal structure of the complex formed beween a group I phosphol... -

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Basic information

Entry
Database: PDB / ID: 1zm6
TitleCrystal structure of the complex formed beween a group I phospholipase A2 and designed penta peptide Leu-Ala-Ile-Tyr-Ser at 2.6A resolution
Components
  • Phospholipase A2 isoform 3
  • designed penta peptide Leu-Ala-Ile-Tyr-Ser
KeywordsHYDROLASE / peptide design / inhibitor
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / phospholipid binding / calcium ion binding / 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
ACETATE ION / Acidic phospholipase A2 3
Similarity search - Component
Biological speciesNaja sagittifera (cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSingh, R.K. / Singh, N. / Jabeen, T. / Sharma, S. / Dey, S. / Singh, T.P.
CitationJournal: J.Drug Target. / Year: 2005
Title: Crystal structure of the complex of group I PLA2 with a group II-specific peptide Leu-Ala-Ile-Tyr-Ser (LAIYS) at 2.6 A resolution.
Authors: Singh, R.K. / Singh, N. / Jabeen, T. / Sharma, S. / Dey, S. / Singh, T.P.
History
DepositionMay 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 isoform 3
P: designed penta peptide Leu-Ala-Ile-Tyr-Ser
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9155
Polymers13,7382
Non-polymers1773
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-5 kcal/mol
Surface area7070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.624, 42.624, 65.203
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Phospholipase A2 isoform 3 / Phosphatidylcholine 2-acylhydrolase / Fragment


Mass: 13172.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja sagittifera (cobra) / References: UniProt: P60045, phospholipase A2
#2: Protein/peptide designed penta peptide Leu-Ala-Ile-Tyr-Ser


Mass: 565.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized.
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10mM phosphate buffer, 20% ethenol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 6, 2003 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 3306 / Num. obs: 3306 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 47.7 Å2
Reflection shellResolution: 2.6→2.65 Å / % possible all: 91

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.36 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 721920.77 / 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
Rfree0.232 176 5.3 %RANDOM
Rwork0.183 ---
all0.212 3306 --
obs0.183 3306 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 94.7932 Å2 / ksol: 0.409735 e/Å3
Displacement parametersBiso mean: 37.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms953 0 12 60 1025
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it2.761.5
X-RAY DIFFRACTIONc_mcangle_it4.452
X-RAY DIFFRACTIONc_scbond_it3.92
X-RAY DIFFRACTIONc_scangle_it5.822.5
LS refinement shellHighest resolution: 2.6 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork399 -
Rfree-6.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramwater.top
X-RAY DIFFRACTION3water_rep.paramacy.top
X-RAY DIFFRACTION4acy.paramion.top

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