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- PDB-3cbi: Crystal structure of the ternary complex of phospholipase A2 with... -

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Basic information

Entry
Database: PDB / ID: 3cbi
TitleCrystal structure of the ternary complex of phospholipase A2 with ajmaline and anisic acid at 3.1 A resolution
ComponentsPhospholipase A2 VRV-PL-VIIIa
KeywordsHYDROLASE / PLA2 / TERNARY COMPLEX / AJMALINE / ANISIC ACID / PHOSPHOLIPASE A2 / Calcium / Lipid degradation / Metal-binding / Neurotoxin / Presynaptic neurotoxin / Secreted / Toxin
Function / homology
Function and homology information


phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / 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
AJMALINE / 4-METHOXYBENZOIC ACID / Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii pulchella (snake)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsKumar, S. / Vikram, G. / Singh, N. / Sharma, S. / Kaur, P. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of the ternary complex of phospholipase A2 with ajmaline and anisic acid at 3.1 A resolution
Authors: Kumar, S. / Vikram, G. / Singh, N. / Sharma, S. / Kaur, P. / Singh, T.P.
History
DepositionFeb 22, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2 VRV-PL-VIIIa
B: Phospholipase A2 VRV-PL-VIIIa
C: Phospholipase A2 VRV-PL-VIIIa
D: Phospholipase A2 VRV-PL-VIIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,32112
Polymers54,5194
Non-polymers1,8028
Water0
1
A: Phospholipase A2 VRV-PL-VIIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0803
Polymers13,6301
Non-polymers4512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phospholipase A2 VRV-PL-VIIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0803
Polymers13,6301
Non-polymers4512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phospholipase A2 VRV-PL-VIIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0803
Polymers13,6301
Non-polymers4512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Phospholipase A2 VRV-PL-VIIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0803
Polymers13,6301
Non-polymers4512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.799, 108.799, 43.339
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Phospholipase A2 VRV-PL-VIIIa / Phosphatidylcholine 2- acylhydrolase / DPLA2


Mass: 13629.767 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / Species: Daboia russellii / Strain: pulchella / References: UniProt: P59071, phospholipase A2
#2: Chemical
ChemComp-AJM / AJMALINE / Ajmaline


Mass: 298.379 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H22N2O2 / Comment: antiarrhythmic, alkaloid*YM
#3: Chemical
ChemComp-ANN / 4-METHOXYBENZOIC ACID / P-ANISIC ACID / P-Anisic acid


Mass: 152.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H8O3

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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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M AMMONIUM SULPHATE, 30% PEG-4K, 0.1M SODIUM ACETATE BUFFER, pH 4.6, 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: Jun 18, 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: 3.15→50 Å / Num. all: 9938 / Num. obs: 9673 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.109 / Net I/σ(I): 4
Reflection shellResolution: 3.15→3.2 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.321 / % possible all: 97.8

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Processing

Software
NameClassification
DENZOdata reduction
AMoREphasing
CNSrefinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OTF

2otf


Resolution: 3.15→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 513 -RANDOM
Rwork0.2276 ---
all0.2331 9673 --
obs-9160 92.2 %-
Displacement parametersBiso mean: 34.5 Å2
Refinement stepCycle: LAST / Resolution: 3.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3772 0 132 0 3904

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