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- PDB-4e4c: Crystal structure of Notexin at 1.8 A resolution -

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Basic information

Entry
Database: PDB / ID: 4e4c
TitleCrystal structure of Notexin at 1.8 A resolution
ComponentsPhospholipase A2
KeywordsHYDROLASE
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / phospholipid binding / 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
Basic phospholipase A2 notexin
Similarity search - Component
Biological speciesNotechis scutatus scutatus (cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsUllah, A. / Spencer, P. / Murakami, M.T. / Arni, R.K.
CitationJournal: To be Published
Title: High resolution structure of Notexin
Authors: Ullah, A. / Spencer, P. / Murakami, M.T. / Arni, R.K.
History
DepositionMar 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0004
Polymers13,6121
Non-polymers3873
Water1,54986
1
A: Phospholipase A2
hetero molecules

A: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0008
Polymers27,2252
Non-polymers7756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area1830 Å2
ΔGint-64 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.100, 74.100, 48.738
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

DetailsTHE BIOLOGICAL ASSEMBLY IS UNKNOWN AS PER AUTHORS

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Components

#1: Protein Phospholipase A2 / / Notexin / Phosphatidylcholine 2-acylhydrolase


Mass: 13612.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Notechis scutatus scutatus (cobra) / References: UniProt: P00608, phospholipase A2
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, 2.5 ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.46 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 10, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.46 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 16425 / Num. obs: 13984 / % possible obs: 95.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.074
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.377 / % possible all: 99.9

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Processing

Software
NameVersionClassification
NatXraysoftwaredata collection
MOLREPphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AE7

1ae7


Resolution: 1.8→26.8 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.848 / SU B: 4.505 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.32247 683 5 %RANDOM
Rwork0.26275 ---
obs0.26569 13045 93.77 %-
all-13045 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.623 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.11 Å20 Å2
2--0.21 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 22 86 1044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022989
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9541338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7255117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86123.87849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.90815155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.898155
X-RAY DIFFRACTIONr_chiral_restr0.1160.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021766
X-RAY DIFFRACTIONr_mcbond_it1.0361.5584
X-RAY DIFFRACTIONr_mcangle_it1.8612928
X-RAY DIFFRACTIONr_scbond_it2.8643405
X-RAY DIFFRACTIONr_scangle_it4.424.5410
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 55 -
Rwork0.358 975 -
obs--96.62 %

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