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- PDB-1mc2: monomeric LYS-49 phospholipase A2 homologue purified from AG -

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Basic information

Entry
Database: PDB / ID: 1mc2
Titlemonomeric LYS-49 phospholipase A2 homologue purified from AG
ComponentsAcutohaemonlysin
KeywordsTOXIN / YS49-PHOSPHOLIPASE A2 / SNAKE VENOM / AGKISTRODON ACUTUS
Function / homology
Function and homology information


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
ISOPROPYL ALCOHOL / Basic phospholipase A2 homolog acutohaemolysin
Similarity search - Component
Biological speciesDeinagkistrodon acutus (Chinese moccasin)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 0.85 Å
AuthorsLiu, Q. / Huang, Q.Q. / Zhang, R.G. / Weeks, C.M. / Jelsch, C. / Teng, M.K. / Niu, L.W.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The crystal structure of a novel, inactive, lysine 49 PLA2 from Agkistrodon acutus venom: an ultrahigh resolution, AB initio structure determination
Authors: Liu, Q. / Huang, Q.Q. / Teng, M.K. / Weeks, C.M. / Jelsch, C. / Zhang, R.G. / Niu, L.W.
History
DepositionAug 5, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acutohaemonlysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2143
Polymers14,0931
Non-polymers1202
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.732, 59.086, 45.308
Angle α, β, γ (deg.)90.00, 117.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2004-

HOH

21A-2044-

HOH

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Components

#1: Protein Acutohaemonlysin / phospholipase a2


Mass: 14093.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinagkistrodon acutus (Chinese moccasin) / References: UniProt: O57385
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 1.45 Å3/Da / Density % sol: 15.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG4000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 5.6 / Details: Huang, Q.Q., (2000) Acta Crystallogr., D56, 907.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %(v/v)2-propanol1reservoir
220 %(w/v)PEG40001reservoir
30.1 Msodium citrate1reservoirpH5.6
420-30 mg/mlprotein1drop
518 %(w/v)PEG40001drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 1999
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.85→10 Å / Num. all: 155596 / Num. obs: 73203 / % possible obs: 79.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.03 / Rsym value: 0.027
Reflection shellResolution: 0.8→0.83 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 0.332 / % possible all: 30
Reflection
*PLUS
Highest resolution: 0.8 Å / Lowest resolution: 20 Å / Num. obs: 84242 / % possible obs: 76.6 % / Num. measured all: 384478 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 34.7 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 0.367

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SHELXL-97refinement
RefinementMethod to determine structure: AB INITIO / Resolution: 0.85→10 Å / Num. parameters: 11281 / Num. restraintsaints: 13526 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 4 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 5.12% (include all data)
RfactorNum. reflection% reflectionSelection details
Rfree0.121 3360 -RANDOM
all0.1043 73203 --
obs0.0949 73203 79.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 10 / Occupancy sum hydrogen: 945 / Occupancy sum non hydrogen: 1210
Refinement stepCycle: LAST / Resolution: 0.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 0 236 2255
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0263
X-RAY DIFFRACTIONs_zero_chiral_vol0.109
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.155
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.131
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.036
X-RAY DIFFRACTIONs_approx_iso_adps0.083
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 0.8 Å / Lowest resolution: 20 Å / Rfactor Rwork: 0.1052
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0188
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.1789
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg0.7973

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