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- PDB-3bjw: Crystal Structure of ecarpholin S complexed with suramin -

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Basic information

Entry
Database: PDB / ID: 3bjw
TitleCrystal Structure of ecarpholin S complexed with suramin
ComponentsPhospholipase A2
KeywordsHYDROLASE / snake venom / Phospholipase A2 / suramin / Ser49 / complex / Calcium / Lipid degradation / Metal-binding / Secreted / Toxin
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / 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
Chem-SVR / Basic phospholipase A2 homolog ecarpholin S
Similarity search - Component
Biological speciesEchis carinatus (saw-scaled viper)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsZhou, X. / Sivaraman, J.
CitationJournal: Biophys.J. / Year: 2008
Title: Structural Characterization of Myotoxic Ecarpholin S from Echis carinatus Venom
Authors: Zhou, X. / Tan, T.C. / Valiyaveettil, S. / Go, M.L. / Kini, R.M. / Velazquez-Campoy, A. / Sivaraman, J.
History
DepositionDec 4, 2007Deposition site: RCSB / Processing site: PDBJ
SupersessionDec 18, 2007ID: 2QHG
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2
B: Phospholipase A2
C: Phospholipase A2
D: Phospholipase A2
E: Phospholipase A2
F: Phospholipase A2
G: Phospholipase A2
H: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,27820
Polymers110,7118
Non-polymers15,56712
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31990 Å2
ΔGint-526.4 kcal/mol
Surface area42850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.450, 132.250, 86.100
Angle α, β, γ (deg.)90.000, 99.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phospholipase A2 / Ecarpholin S / Phosphatidylcholine 2-acylhydrolase


Mass: 13838.879 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Echis carinatus (saw-scaled viper) / References: UniProt: P48650, phospholipase A2
#2: Chemical
ChemComp-SVR / 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID / SURAMIN


Mass: 1297.280 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C51H40N6O23S6 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.6
Details: 10% PEG3350, 10% iso-propanol, 0.1M sodium citrate, the ratio of suramin to protein is 1.5:1, pH5.6, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 12, 2006 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 55923 / % possible obs: 97.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.089 / Χ2: 0.998 / Net I/σ(I): 8.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.386 / Num. unique all: 4937 / Χ2: 0.918 / % possible all: 86.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JIA

1jia


Resolution: 2.3→20 Å / FOM work R set: 0.796 / σ(F): 4322
RfactorNum. reflection% reflection
Rfree0.275 4538 9 %
Rwork0.217 --
obs-45082 89.6 %
Solvent computationBsol: 32.932 Å2
Displacement parametersBiso mean: 33.702 Å2
Baniso -1Baniso -2Baniso -3
1--1.335 Å20 Å2-1.216 Å2
2--0.579 Å20 Å2
3---0.756 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7672 0 1032 370 9074
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.482
X-RAY DIFFRACTIONc_mcbond_it1.0571.5
X-RAY DIFFRACTIONc_scbond_it1.6482
X-RAY DIFFRACTIONc_mcangle_it1.7062
X-RAY DIFFRACTIONc_scangle_it2.3472.5
Refine LS restraints NCSRms: 0 / Type: restrain / Weight: 300
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4svr.paramsvr.top

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