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- PDB-1g2x: Sequence induced trimerization of krait PLA2: crystal structure o... -

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Basic information

Entry
Database: PDB / ID: 1g2x
TitleSequence induced trimerization of krait PLA2: crystal structure of the trimeric form of krait PLA2
ComponentsPHOSPHOLIPASE A2
KeywordsTOXIN / Phospholipase A2 / Homotrimer / Bungarus caeruleus
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, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Basic phospholipase A2 3 / Basic phospholipase A2 KPA2
Similarity search - Component
Biological speciesBungarus caeruleus (cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSingh, G. / Gourinath, S. / Sharma, S. / Bhanumathi, S. / Paramsivam, M. / Singh, T.P.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Sequence-induced trimerization of phospholipase A2: structure of a trimeric isoform of PLA2 from common krait (Bungarus caeruleus) at 2.5 A resolution.
Authors: Singh, G. / Gourinath, S. / Saravanan, K. / Sharma, S. / Bhanumathi, S. / Betzel, C.h. / Srinivasan, A. / Singh, T.P.
#1: Journal: To be Published
Title: Specific mutations in Krait PLA2 lead to dimerization of protein molecules: Crystal structure of Krait PLA2 at 2.1 resolution.
Authors: Gourinath, S. / Singh, G. / Sharma, S. / Bhanumathi, S. / Betzel, C. / Paramsivam, M. / Srinivasan, A. / Singh, T.P.
#2: Journal: To be Published
Title: Three-dimensional structure of a novel phospholipase A2 from Indian common krait at 2.45 resolution.
Authors: Singh, G. / Gourinath, S. / Sharma, S. / Paramasivam, M. / Srinivasan, A. / Singh, T.P.
History
DepositionOct 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2
B: PHOSPHOLIPASE A2
C: PHOSPHOLIPASE A2


Theoretical massNumber of molelcules
Total (without water)38,9543
Polymers38,9543
Non-polymers00
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.949, 80.572, 57.098
Angle α, β, γ (deg.)90.00, 90.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-178-

HOH

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Components

#1: Protein PHOSPHOLIPASE A2 /


Mass: 12984.620 Da / Num. of mol.: 3 / Fragment: RESIDUES 28-145 / Source method: isolated from a natural source / Details: NATURAL PROTEIN-ISOFORM / Source: (natural) Bungarus caeruleus (cobra) / Secretion: VENOM
References: UniProt: Q9DF52, UniProt: Q6SLM0*PLUS, phospholipase A2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM Tris.HCl, 3.0 M NaCl, 1mM NaN3, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 281.0K
Crystal grow
*PLUS
Temperature: 281 K / pH: 8.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
250 mMTris-HCl1droppH8.5
31.4 M1dropNaCl
41 mM1dropNaN3
52.8 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 22, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 12779 / Num. obs: 12745 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.98 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 0.091 / Net I/σ(I): 7.8
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 4.98 % / Num. unique all: 12779 / Rsym value: 0.203 / % possible all: 99.6
Reflection
*PLUS
Rmerge(I) obs: 0.091
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1FE5

1fe5


Resolution: 2.5→14.28 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 13123.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 644 5.1 %RANDOM
Rwork0.198 ---
all0.201 12779 --
obs0.198 12533 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 85.03 Å2 / ksol: 0.472 e/Å3
Displacement parametersBiso mean: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20.69 Å2
2--1.75 Å20 Å2
3----0.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.25 Å
Luzzati d res low-4 Å
Luzzati sigma a0.36 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.5→14.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2694 0 0 258 2952
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 79 5.4 %
Rwork0.213 1372 -
obs--64.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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