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- PDB-1oyf: Crystal Structure of Russelles viper (Daboia russellii pulchella)... -

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Basic information

Entry
Database: PDB / ID: 1oyf
TitleCrystal Structure of Russelles viper (Daboia russellii pulchella) phospholipase A2 in a complex with venom 6-methyl heptanol
Components(Phospholipase ...) x 2
KeywordsHYDROLASE / Phospholipase A2 / complex / Catalysis / Inhibition
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonic acid 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
ACETIC ACID / 6-METHYLHEPTAN-1-OL / Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii pulchella (snake)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSingh, N. / Jabeen, T. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal Structure of Russelles viper (Daboia russellii pulchella) phospholipase A2 in a complex with venom 6-methyl heptanol
Authors: Singh, N. / Jabeen, T. / Sharma, S. / Singh, T.P.
History
DepositionApr 4, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,7316
Polymers27,3152
Non-polymers4174
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.866, 69.071, 75.646
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Phospholipase ... , 2 types, 2 molecules AB

#1: Protein Phospholipase A2 /


Mass: 13656.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / Secretion: Venom / Species: russellii / Strain: pulchella / References: UniProt: P59071, phospholipase A2
#2: Protein Phospholipase A2 /


Mass: 13657.780 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / Secretion: Venom / Species: russellii / Strain: pulchella / References: phospholipase A2

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Non-polymers , 4 types, 152 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MHN / 6-METHYLHEPTAN-1-OL / METHYL HEPTANOL


Mass: 130.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Cacodylate buffer, 0.2M Ammonoum Sulphate, 15% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 4, 2002 / Details: Monochromator
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 58251 / Num. obs: 7984 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 18.9 Å2 / Rsym value: 0.072 / Net I/σ(I): 25.2
Reflection shellResolution: 2.4→2.5 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.31 / % possible all: 95.3

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVO

1fvo


Resolution: 2.45→19.86 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 173506.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Trp31 im molecule A is having double positions. Both were refined separately. The distance between the C of GLY A 30 and alternate conformation B of TRP A 31 is long.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 390 5.3 %RANDOM
Rwork0.192 ---
all0.195 7345 --
obs0.192 7345 79.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.0431 Å2 / ksol: 0.347483 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.45→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 27 148 2067
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg2.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_mcbond_it2.041.5
X-RAY DIFFRACTIONc_mcangle_it3.272
X-RAY DIFFRACTIONc_scbond_it3.182
X-RAY DIFFRACTIONc_scangle_it4.722.5
LS refinement shellResolution: 2.44→2.59 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.211 18 4.3 %
Rwork0.278 398 -
obs--27.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CSP.PARAMCSP.TOP
X-RAY DIFFRACTION5SUL.PARAMSUL.TOP

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