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- PDB-7m6c: Crystal structure of PLA2 from snake venom of peruvian Bothrops atrox -

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Basic information

Entry
Database: PDB / ID: 7m6c
TitleCrystal structure of PLA2 from snake venom of peruvian Bothrops atrox
ComponentsBasic phospholipase A2
KeywordsTOXIN / HYDROLASE / phospholipase / snake venom
Function / homology
Function and homology information


phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / 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 domain superfamily
Similarity search - Domain/homology
LAURIC ACID / BATXPLA2
Similarity search - Component
Biological speciesBothrops atrox (barba amarilla)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLeonardo, D.A. / Chojnowski, G. / Simpkin, A. / Seifert-Davila, W. / Vivas-Ruiz, D.E. / Keegan, R. / Rigden, D.
CitationJournal: Iucrj / Year: 2022
Title: findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM
Authors: Chojnowski, G. / Simpkin, A. / Leonardo, D.A. / Seifert-Davila, W. / Vivas-Ruiz, D.E. / Keegan, R. / Rigden, D.
History
DepositionMar 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Basic phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8422
Polymers15,6411
Non-polymers2001
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.400, 58.360, 64.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Basic phospholipase A2


Mass: 15641.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bothrops atrox (barba amarilla) / References: UniProt: A0A1L8D5Z7, phospholipase A2
#2: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20% (v/v) 2-propanol, 20% (w/v) polyethylene Glycol 4000 and 0.1 M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45863 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45863 Å / Relative weight: 1
ReflectionResolution: 1.95→43.263 Å / Num. all: 10474 / Num. obs: 10474 / % possible obs: 99.7 % / Redundancy: 4 % / Rpim(I) all: 0.062 / Rrim(I) all: 0.126 / Rsym value: 0.099 / Net I/av σ(I): 2 / Net I/σ(I): 5.8 / Num. measured all: 41934
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.95-2.064.10.3221.5613314890.1930.4030.3222.299.9
2.06-2.183.90.2971.7553914330.1910.3940.2973.199.9
2.18-2.334.10.2192.4539013260.1340.2750.2193.8100
2.33-2.5240.1883.1503412490.1090.2280.1884.599.8
2.52-2.7640.1464.2464211740.0850.1770.1465.399.9
2.76-3.084.10.1125.2437310550.0650.1350.112799.6
3.08-3.563.80.1045.635039300.0620.1270.104999.7
3.56-4.364.30.05210.834348060.030.0650.05211.799.2
4.36-6.173.90.03615.824426340.0220.0450.03610.398.9
6.17-43.2633.80.0681.314443780.0570.0920.06810.598

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
SCALAdata scaling
SIMBADphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MC2

1mc2


Resolution: 1.95→43.263 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.19 / SU B: 8.226 / SU ML: 0.119 / Average fsc free: 0.9107 / Average fsc work: 0.9207 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.161 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 1099 10.516 %RANDOM
Rwork0.1869 9352 --
all0.192 ---
obs-10451 99.505 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.034 Å2
Baniso -1Baniso -2Baniso -3
1-0.431 Å20 Å2-0 Å2
2---0.32 Å20 Å2
3----0.111 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 14 100 1072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121004
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.6681347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2965123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85722.95544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16115198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.762155
X-RAY DIFFRACTIONr_chiral_restr0.120.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02729
X-RAY DIFFRACTIONr_nbd_refined0.2180.2508
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2683
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2106
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1830.222
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.210
X-RAY DIFFRACTIONr_mcbond_it1.62.045489
X-RAY DIFFRACTIONr_mcangle_it2.713.057610
X-RAY DIFFRACTIONr_scbond_it1.9482.323515
X-RAY DIFFRACTIONr_scangle_it3.1473.356736
X-RAY DIFFRACTIONr_lrange_it6.11828.7941632
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.95-2.0010.315730.2796810.2837540.7830.8231000.265
2.001-2.0550.249650.2566680.2557340.8760.85199.86380.243
2.055-2.1150.3760.2396420.2457180.8360.8761000.23
2.115-2.180.242580.2386510.2387110.8930.8899.71870.223
2.18-2.2510.259770.1935920.26690.8890.9221000.18
2.251-2.330.222680.1785880.1836560.930.9341000.17
2.33-2.4170.241680.1885730.1946430.930.93499.6890.18
2.417-2.5160.233750.1715280.1796030.9250.941000.164
2.516-2.6270.244680.1745350.1826040.9210.93999.83440.169
2.627-2.7550.238650.1865020.1925670.9370.941000.179
2.755-2.9030.232490.1784840.1835350.9370.95199.62620.173
2.903-3.0790.226620.1934590.1975260.930.94499.04940.188
3.079-3.290.202520.1694220.1734740.9560.9561000.17
3.29-3.5520.246460.1744010.184510.9240.95299.11310.172
3.552-3.8880.218430.1713830.1764360.9440.95797.70640.173
3.888-4.3430.17310.1573490.1583820.9640.96799.47640.161
4.343-5.0060.169390.152970.1523420.9710.97598.24560.153
5.006-6.1110.234370.1882610.1933030.9520.96198.34980.19
6.111-8.5570.265380.1741980.1892400.950.96798.33330.178
8.557-43.2630.50490.2221370.2321540.8950.94694.80520.487
Refinement TLS params.Method: refined / Origin x: 10.1316 Å / Origin y: 22.0155 Å / Origin z: 19.4821 Å
111213212223313233
T0.0302 Å2-0.0039 Å20.0186 Å2-0.0164 Å2-0.0034 Å2--0.0128 Å2
L1.0486 °2-0.4478 °2-0.6881 °2-1.7776 °20.6685 °2--0.5404 °2
S-0.0258 Å °0.1116 Å °-0.0092 Å °0.0077 Å °0.0146 Å °-0.0245 Å °0.0248 Å °-0.0611 Å °0.0112 Å °
Refinement TLS groupSelection: ALL

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