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- PDB-2ph4: Crystal structure of a novel Arg49 phospholipase A2 homologue fro... -

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Basic information

Entry
Database: PDB / ID: 2ph4
TitleCrystal structure of a novel Arg49 phospholipase A2 homologue from Zhaoermia mangshanensis venom
ComponentsZhaoermiatoxin
KeywordsTOXIN / snake venom / arg49 / phospholipase A2 / myotoxin
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 / toxin activity / 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
DI(HYDROXYETHYL)ETHER / Basic phospholipase A2 homolog zhaoermiatoxin
Similarity search - Component
Biological speciesZhaoermia mangshanensis (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMurakami, M.T. / Kuch, U. / Mebs, D. / Arni, R.K.
CitationJournal: Toxicon / Year: 2008
Title: Crystal structure of a novel myotoxic Arg49 phospholipase A(2) homolog (zhaoermiatoxin) from Zhaoermia mangshanensis snake venom: Insights into Arg49 coordination and the role of Lys122 in the ...Title: Crystal structure of a novel myotoxic Arg49 phospholipase A(2) homolog (zhaoermiatoxin) from Zhaoermia mangshanensis snake venom: Insights into Arg49 coordination and the role of Lys122 in the polarization of the C-terminus.
Authors: Murakami, M.T. / Kuch, U. / Betzel, C. / Mebs, D. / Arni, R.K.
History
DepositionApr 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999sequence THE SEQUENCE IS NUMBERED BASED ON THE BOVINE PANCREATIC PHOSPHOLIPASE A2. SO, NOT ...sequence THE SEQUENCE IS NUMBERED BASED ON THE BOVINE PANCREATIC PHOSPHOLIPASE A2. SO, NOT SEQUENTIAL NUMBERS INDICATE DELETIONS AND INSERTIONS REGIONS IN COMPARISON WITH BOVINE PANCREATIC PLA2.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zhaoermiatoxin
B: Zhaoermiatoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7139
Polymers28,0212
Non-polymers6937
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-81 kcal/mol
Surface area12610 Å2
MethodPISA
2
A: Zhaoermiatoxin
B: Zhaoermiatoxin
hetero molecules

A: Zhaoermiatoxin
B: Zhaoermiatoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,42718
Polymers56,0424
Non-polymers1,38514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.933, 72.933, 93.938
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
DetailsThe biological assembly is the dimer found in the asymmetric unit.

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Components

#1: Protein Zhaoermiatoxin / Phospholipase A2 homolog


Mass: 14010.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Zhaoermia mangshanensis (snake) / Secretion: venom / References: UniProt: P84776
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: polyethylene glycol 8,000; ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 2.05→23.87 Å / Num. obs: 17731 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 12.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 33.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.8 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y4L

1y4l


Resolution: 2.05→23.87 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.883 / SU B: 5.84 / SU ML: 0.16 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2886 1800 10.2 %RANDOM
Rwork0.20942 ---
obs0.21729 15931 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.077 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.49 Å20 Å2
2--0.98 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.05→23.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 39 235 2214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222030
X-RAY DIFFRACTIONr_angle_refined_deg2.2231.9982727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.6765242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52123.33384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.20215389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.451514
X-RAY DIFFRACTIONr_chiral_restr0.1380.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021466
X-RAY DIFFRACTIONr_nbd_refined0.2450.21339
X-RAY DIFFRACTIONr_nbtor_refined0.3280.21404
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.2267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3090.221
X-RAY DIFFRACTIONr_mcbond_it1.1271.51248
X-RAY DIFFRACTIONr_mcangle_it1.82921948
X-RAY DIFFRACTIONr_scbond_it3.0683907
X-RAY DIFFRACTIONr_scangle_it4.1634.5778
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 150 -
Rwork0.239 1173 -
obs--99.77 %

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