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- PDB-5vfj: Crystal structure of BnSP-7 from bothrops pauloensis complexed wi... -

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Basic information

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


phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / 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
CAFFEIC ACID / Basic phospholipase A2 homolog BnSP-7
Similarity search - Component
Biological speciesBothrops pauloensis (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.084 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 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code ..._struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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
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)28,1658
Polymers27,5042
Non-polymers6606
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-83 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.574, 59.060, 58.460
Angle α, β, γ (deg.)90.00, 95.78, 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DHC / CAFFEIC ACID / 3,4-DIHYDROXYCINNAMIC ACID / Caffeic acid


Mass: 180.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% polyethylene glycol 4000, 100 mM TrisHCl pH 8.5 and 200 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: Jul 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.4591
21.51
ReflectionResolution: 2.084→26.33 Å / Num. obs: 18143 / % possible obs: 97.63 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 4.37
Reflection shellResolution: 2.084→2.158 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.458 / Num. unique obs: 1633 / % possible all: 88.8

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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: 2.084→26.33 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.87
RfactorNum. reflection% reflection
Rfree0.2402 908 5.01 %
Rwork0.2062 --
obs0.208 18125 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.084→26.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 38 227 2135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041957
X-RAY DIFFRACTIONf_angle_d0.9232617
X-RAY DIFFRACTIONf_dihedral_angle_d12.788728
X-RAY DIFFRACTIONf_chiral_restr0.036266
X-RAY DIFFRACTIONf_plane_restr0.004335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0835-2.2140.31541400.25712665X-RAY DIFFRACTION92
2.214-2.38480.30491510.23512874X-RAY DIFFRACTION98
2.3848-2.62460.2521550.22472907X-RAY DIFFRACTION100
2.6246-3.0040.26051530.21472928X-RAY DIFFRACTION99
3.004-3.78290.22381540.19882916X-RAY DIFFRACTION99
3.7829-26.33280.20731550.1832927X-RAY DIFFRACTION98
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)
16.15760.82391.66436.0191-1.77611.2545-0.2899-0.19550.2698-0.17130.381-0.0062-0.08-0.2994-0.04070.2217-0.02620.01350.2577-0.02420.16912.633716.645464.9539
23.82932.661-0.45572.9135-0.18658.1735-0.0617-0.7135-0.590.27940.2130.032-0.04490.0076-0.23760.2327-0.01030.00060.29470.02030.46564.07123.126473.3737
33.8419-1.213-2.09333.74872.58633.4668-0.0882-0.3205-0.04370.5308-0.0576-0.05880.1029-0.40610.11820.27090.0188-0.01580.37610.05510.25046.325314.866477.7251
42.8987-0.8824-2.19171.25161.57292.45590.1906-0.0920.65110.10460.1536-0.1392-0.81140.4832-0.51650.4199-0.04620.00060.274-0.00580.443211.241527.366967.6993
52.2243-0.6512-0.4936.28322.31741.91770.0243-0.1233-0.06880.1073-0.0678-0.05050.0764-0.3048-0.03870.2522-0.0174-0.00490.27980.05020.27179.719113.314769.1479
60.85550.6445-2.09013.7472-1.6675.47420.05340.1046-0.241-0.1717-0.5063-0.18670.4756-0.71110.57540.2523-0.05260.02490.4372-0.00990.5247-2.5367-0.504670.2339
72.82881.1317-1.37967.4610.80193.58560.0475-0.0154-0.65641.272-0.1828-0.9110.06790.39530.3470.4931-0.0808-0.15550.41680.2340.65428.41660.277881.8563
86.7150.7856-0.82253.33571.70741.8893-0.31440.0788-0.3948-0.17540.2973-0.2043-0.04750.28670.03150.24430.01890.01980.2955-0.03640.1867-14.3148-2.887665.3117
92.7961.1222-0.29423.7849-1.97635.82750.0447-0.14240.53140.28930.1172-0.19110.10760.15440.10470.20090.00160.00550.2562-0.0240.334-15.720910.824273.295
102.34850.5814-0.46244.5769-3.05664.79180.0477-0.31950.21530.22010.00390.3110.0428-0.08440.00490.24090.00040.01520.2395-0.06790.3071-20.92964.94576.2102
112.7981.33672.26432.0161.14742.37940.15220.1439-0.34510.40610.00030.01730.52440.524-0.17560.31180.02370.03810.3370.01840.3571-17.2948-9.815573.6673
124.82991.76745.68431.7823.44688.310.5452-0.5905-1.4913-0.04570.0793-0.49751.4138-0.1039-0.72090.4956-0.03710.00340.34710.11480.4477-22.3261-14.233874.8177
133.1146-0.88571.20976.1473-1.4063.2265-0.0589-0.05990.2419-0.09490.2380.09570.215-0.1428-0.2270.13310.01440.02290.2186-0.05340.2123-21.27560.907969.254
140.55440.05080.8392.91071.23791.8445-0.0451-0.07940.20580.2406-0.10360.0865-0.04480.25410.15550.2531-0.0586-0.00670.3838-0.04870.4398-13.607314.21474.8488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 74 )
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 88 )
5X-RAY DIFFRACTION5chain 'A' and (resid 90 through 117 )
6X-RAY DIFFRACTION6chain 'A' and (resid 118 through 125 )
7X-RAY DIFFRACTION7chain 'A' and (resid 126 through 133 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 22 )
9X-RAY DIFFRACTION9chain 'B' and (resid 23 through 39 )
10X-RAY DIFFRACTION10chain 'B' and (resid 40 through 57 )
11X-RAY DIFFRACTION11chain 'B' and (resid 58 through 81 )
12X-RAY DIFFRACTION12chain 'B' and (resid 82 through 88 )
13X-RAY DIFFRACTION13chain 'B' and (resid 90 through 117 )
14X-RAY DIFFRACTION14chain 'B' and (resid 118 through 133 )

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