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- PDB-5vfn: Crystal structure of BnSP-7 from Bothrops pauloensis complexed wi... -

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Basic information

Entry
Database: PDB / ID: 5vfn
TitleCrystal structure of BnSP-7 from Bothrops pauloensis complexed with cinnamic acid
ComponentsBasic phospholipase A2 homolog BnSP-7
KeywordsHYDROLASE / Lys49-PLA2 / Bothrops pauloensis / cinnamic acid
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / defense response to bacterium / 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
HYDROCINNAMIC ACID / 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE / Basic phospholipase A2 homolog BnSP-7
Similarity search - Component
Biological speciesBothrops pauloensis (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.389 Å
AuthorsDe Lima, L.F.G. / Fontes, M.R.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)140501/2014-2 Brazil
CitationJournal: Biochimie / Year: 2017
Title: Structural studies with BnSP-7 reveal an atypical oligomeric conformation compared to phospholipases A2-like toxins.
Authors: de Lima, L.F.G. / Borges, R.J. / Viviescas, M.A. / Fernandes, C.A.H. / Fontes, M.R.M.
History
DepositionApr 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Basic phospholipase A2 homolog BnSP-7
B: Basic phospholipase A2 homolog BnSP-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,52711
Polymers27,5042
Non-polymers1,0239
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.775, 58.655, 58.128
Angle α, β, γ (deg.)90.00, 95.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Basic phospholipase A2 homolog BnSP-7 / svPLA2 homolog / Phospholipase A2 II


Mass: 13752.085 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bothrops pauloensis (snake) / References: UniProt: Q9IAT9
#2: Chemical ChemComp-HCI / HYDROCINNAMIC ACID / 3PP / 3-PHENYLPROPIONIC ACID


Mass: 150.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O2
#3: Chemical ChemComp-ME2 / 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE


Mass: 148.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% polyethylene glycol 4000, 100 mM TrisHCl pH 8.5 and 150 mM lithium sulfate
PH range: 8.3-8.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459, 1.500
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.4591
21.51
ReflectionResolution: 2.389→45.54 Å / Num. obs: 12111 / % possible obs: 98.45 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.175 / Net I/σ(I): 8.47
Reflection shellResolution: 2.389→2.474 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.603 / Num. unique obs: 1084 / % possible all: 87.99

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000v714data reduction
HKL-2000v714data scaling
PHASER2.1phasing
Coot0.8.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1pa0

1pa0


Resolution: 2.389→45.536 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2598 1208 10 %
Rwork0.2169 --
obs0.2212 12086 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.389→45.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 57 97 2012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041961
X-RAY DIFFRACTIONf_angle_d1.0232618
X-RAY DIFFRACTIONf_dihedral_angle_d13.794723
X-RAY DIFFRACTIONf_chiral_restr0.039266
X-RAY DIFFRACTIONf_plane_restr0.005334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3889-2.48450.37821200.31671079X-RAY DIFFRACTION89
2.4845-2.59760.32571340.28141201X-RAY DIFFRACTION99
2.5976-2.73450.27591340.25621214X-RAY DIFFRACTION99
2.7345-2.90580.28391330.2441219X-RAY DIFFRACTION99
2.9058-3.13010.32431350.23141205X-RAY DIFFRACTION99
3.1301-3.4450.26391380.2271232X-RAY DIFFRACTION100
3.445-3.94330.21461370.17891232X-RAY DIFFRACTION100
3.9433-4.96710.22721360.17561231X-RAY DIFFRACTION100
4.9671-45.54420.23951410.21361265X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.77830.24550.20712.14640.63262.2659-0.0562-0.2849-0.250.08520.0571-0.001-0.0291-0.03070.03680.2552-0.00040.00680.32620.06940.340444.95437.2852128.1041
22.4416-0.6005-1.4750.884-1.14484.86080.3866-0.21180.24580.3316-0.2821-0.0467-1.03620.0929-0.1180.461-0.08650.01350.3576-0.08110.371846.832921.89130.3801
32.23370.7275-0.97553.043-0.44320.46820.059-0.0659-0.1730.2385-0.03240.0415-0.0341-0.1621-0.00380.26850.0041-0.0140.32250.05940.225246.9365.5997128.3652
41.90771.1819-0.00761.67390.72642.3785-0.16930.07220.11210.04320.11670.06970.15280.40260.00580.26680.0555-0.03420.29880.01810.356325.8042-2.7864124.8271
52.12381.0503-0.22021.9893-0.6393.3791-0.05580.21470.69660.31370.17070.112-0.14780.0470.00520.26250.0105-0.03330.3501-0.05490.420119.44924.4808133.1067
61.86560.33630.16151.30.27085.67340.2084-0.1237-0.2190.3706-0.0159-0.00731.2632-0.1046-0.08710.409-0.02690.04330.29170.02820.477320.8574-13.9992131.634
72.3088-0.17540.78822.1708-0.59210.32250.04510.29930.3371-0.0228-0.00210.13910.06520.2448-0.02560.27860.00990.03980.3302-0.03710.288721.01042.2891128.5797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 88 )
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 133 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 32 )
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 57 )
6X-RAY DIFFRACTION6chain 'B' and (resid 58 through 88 )
7X-RAY DIFFRACTION7chain 'B' and (resid 90 through 133 )

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