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- PDB-1q5t: Gln48 PLA2 separated from Vipoxin from the venom of Vipera ammody... -

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Basic information

Entry
Database: PDB / ID: 1q5t
TitleGln48 PLA2 separated from Vipoxin from the venom of Vipera ammodytes meridionalis.
ComponentsPhospholipase A2 inhibitor
KeywordsTOXIN
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / negative regulation of T cell proliferation / phospholipid metabolic process / 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 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Acidic phospholipase A2 homolog vipoxin A chain
Similarity search - Component
Biological speciesVipera ammodytes meridionalis (snake)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGeorgieva, D.N. / Perbandt, M. / Rypniewski, W. / Hristov, K. / Genov, N. / Betzel, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: The X-ray structure of a snake venom Gln48 phospholipase A2 at 1.9A resolution reveals anion-binding sites.
Authors: Georgieva, D.N. / Perbandt, M. / Rypniewski, W. / Hristov, K. / Genov, N. / Betzel, C.
History
DepositionAug 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
Remark 999SEQUENCE The sequence conflicts may be due to a different interpretation of experimental data ...SEQUENCE The sequence conflicts may be due to a different interpretation of experimental data and/or evolutionary gene mutations.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2 inhibitor
B: Phospholipase A2 inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6806
Polymers27,2962
Non-polymers3844
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-81 kcal/mol
Surface area11080 Å2
MethodPISA
2
A: Phospholipase A2 inhibitor
B: Phospholipase A2 inhibitor
hetero molecules

A: Phospholipase A2 inhibitor
B: Phospholipase A2 inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,36112
Polymers54,5924
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z+1/21
Buried area8800 Å2
ΔGint-171 kcal/mol
Surface area20950 Å2
MethodPISA
3
A: Phospholipase A2 inhibitor
B: Phospholipase A2 inhibitor
hetero molecules

A: Phospholipase A2 inhibitor
B: Phospholipase A2 inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,36112
Polymers54,5924
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z+1/21
Buried area8830 Å2
ΔGint-159 kcal/mol
Surface area20930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.948, 58.948, 139.119
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-542-

HOH

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Components

#1: Protein Phospholipase A2 inhibitor / Vipoxin toxic component / Vipoxin A chain / Inh


Mass: 13648.102 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vipera ammodytes meridionalis (snake) / Secretion: venom / Species: Vipera ammodytes / Strain: meridionalis / References: UniProt: P04084
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.43 %

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 20703

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Processing

SoftwareName: REFMAC / Version: 5.1.24 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→10 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.98 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25384 956 5.1 %RANDOM
Rwork0.18542 ---
all0.18899 ---
obs0.18899 17790 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.598 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2---0.74 Å20 Å2
3---1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 20 336 2250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211962
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.091.9482662
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2545242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1450.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021547
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.21102
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2247
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1451.51200
X-RAY DIFFRACTIONr_mcangle_it1.96221903
X-RAY DIFFRACTIONr_scbond_it3.3153762
X-RAY DIFFRACTIONr_scangle_it5.0174.5759
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.385 64
Rwork0.391 1230

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