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- PDB-3fg5: Crystal structure determination of a ternary complex of phospholi... -

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Basic information

Entry
Database: PDB / ID: 3fg5
TitleCrystal structure determination of a ternary complex of phospholipase A2 with a pentapeptide FLSYK and Ajmaline at 2.5 A resolution
Components
  • Group II Phospholipase A2
  • pentapeptide FLSYK
KeywordsHYDROLASE / pla2 / pentapeptide / FLSYK / ajmaline / ternary complex
Function / homologyPhospholipase A2 / Phospholipase A2 domain / Up-down Bundle / Mainly Alpha / AJMALINE
Function and homology information
Biological speciesDaboia russelli pulchella (snake)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKumar, M. / Kumar, S. / Vikram, G. / Singh, N. / Sinha, M. / Bhushan, A. / Kaur, P. / Srinivasan, A. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure determination of a ternary complex of phospholipase A2 with a pentapeptide FLSYK and Ajmaline at 2.5 A resolution
Authors: Kumar, M. / Kumar, S. / Vikram, G. / Singh, N. / Sinha, M. / Bhushan, A. / Kaur, P. / Srinivasan, A. / Sharma, S. / Singh, T.P.
History
DepositionDec 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Group II Phospholipase A2
C: pentapeptide FLSYK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5863
Polymers14,2882
Non-polymers2981
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-2 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.949, 52.949, 48.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Group II Phospholipase A2


Mass: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russelli pulchella (snake) / References: phospholipase A2
#2: Protein/peptide pentapeptide FLSYK


Mass: 657.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHESIZED SHORT PEPTIDE
#3: Chemical ChemComp-AJM / AJMALINE


Mass: 298.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE OF ENTITY 1 IS THE SAME WITH UNP P59071 PA28_DABRP, WHICH HAS DIFFERENT SOURCE.

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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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.2M AMMONIUM SULPHATE, 0.2M AMMONIUM ACETATE, 30% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 2, 2007 / 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: 2.5→20 Å / Num. all: 4639 / Num. obs: 4392 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.096 / Net I/σ(I): 6.4
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.439 / % possible all: 98.5

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Processing

Software
NameClassification
DENZOdata reduction
MOLREPphasing
CNSrefinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZR8

1zr8


Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.227 247 -RANDOM
Rwork0.1876 ---
all0.227 4639 --
obs0.188 4392 93.2 %-
Displacement parametersBiso max: 98.14 Å2 / Biso min: 11.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.218 Å20 Å20 Å2
2---1.218 Å20 Å2
3---2.436 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 22 61 1073
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5741.5
X-RAY DIFFRACTIONc_scbond_it2.1422
X-RAY DIFFRACTIONc_mcangle_it2.7022
X-RAY DIFFRACTIONc_scangle_it3.3212.5

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