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- PDB-2i0u: Crystal structures of phospholipases A2 from Vipera nikolskii ven... -

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Basic information

Entry
Database: PDB / ID: 2i0u
TitleCrystal structures of phospholipases A2 from Vipera nikolskii venom revealing Triton X-100 bound in hydrophobic channel
ComponentsBasic subunit of heterodimer phospholipase A2
KeywordsHYDROLASE / alpha-beta-alpha
Function / homology
Function and homology information


phospholipase A2 / 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, histidine active site / Phospholipase A2 histidine active site. / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
trifluoroacetic acid / Basic phospholipase A2 chain HDP-1P
Similarity search - Component
Biological speciesVipera nikolskii (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGao, W. / Bi, R.C.
CitationJournal: To be Published
Title: Crystal structures of phospholipases A2 from Vipera nikolskii venom revealing Triton X-100 bound in hydrophobic channel
Authors: Gao, W. / Bi, R.C.
History
DepositionAug 11, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Basic subunit of heterodimer phospholipase A2
A: Basic subunit of heterodimer phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7519
Polymers27,6602
Non-polymers1,0917
Water3,747208
1
E: Basic subunit of heterodimer phospholipase A2
A: Basic subunit of heterodimer phospholipase A2
hetero molecules

E: Basic subunit of heterodimer phospholipase A2
A: Basic subunit of heterodimer phospholipase A2
hetero molecules

E: Basic subunit of heterodimer phospholipase A2
A: Basic subunit of heterodimer phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,25327
Polymers82,9796
Non-polymers3,27421
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area15400 Å2
ΔGint-160 kcal/mol
Surface area33420 Å2
MethodPISA
2
A: Basic subunit of heterodimer phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3924
Polymers13,8301
Non-polymers5633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: Basic subunit of heterodimer phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3585
Polymers13,8301
Non-polymers5294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)76.284, 76.284, 304.395
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11E-1001-

CA

21E-1334-

HOH

DetailsThe second part of the biological assembly is generated by the three fold axis: x+2/3, y+1/3, z.

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Components

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Protein , 1 types, 2 molecules EA

#1: Protein Basic subunit of heterodimer phospholipase A2 / phospholipases A2


Mass: 13829.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vipera nikolskii (snake) / Secretion: venom / References: UniProt: Q1RP79, phospholipase A2

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Non-polymers , 5 types, 215 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRT / FRAGMENT OF TRITON X-100 / 1-{2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY}-4-(1,1,3,3-TETRAMETHYLBUTYL)BENZENE


Mass: 352.508 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM
#5: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 4K, 0.2M lithium sulphate, 0.1M sodium cacodylate pH 6.5, 0.1% sodium azide, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→29 Å / Num. obs: 17760 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.26 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29 Å / σ(F): 2
RfactorNum. reflection
Rfree0.236 -
Rwork0.209 -
obs0.209 16104
all-17852
Refinement stepCycle: LAST / Resolution: 2.2→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 69 208 2201
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0184
X-RAY DIFFRACTIONc_angle_deg1.67

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