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- PDB-3g8f: Crystal structure of the complex formed between a group II phosph... -

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Basic information

Entry
Database: PDB / ID: 3g8f
TitleCrystal structure of the complex formed between a group II phospholipase A2 and designed peptide inhibitor carbobenzoxy-dehydro-val-ala-arg-ser at 1.2 A resolution
Components
  • PHQ VAL ALA ARG SER peptide
  • Phospholipase A2 VRV-PL-VIIIa
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PHOSPHOLIPASE A2 / CRYSTAL STRUCTRE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


phospholipase A2 / 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
CARBOBENZOXY-DEHYDRO-VAL-ALA-ARG-SER / Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii russellii (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSingh, N. / Kaur, P. / Prem Kumar, R. / Somvanshi, R.K. / Perbandt, M. / Betzel, C. / Dey, S. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal Structure of the Complex Formed between a Group II Phospholipase A2 and Designed Peptide Inhibitor Carbobenzoxy-Dehydro-Val-Ala-Arg-Ser at 1.2 A Resolution
Authors: Singh, N. / Kaur, P. / Prem Kumar, R. / Somvanshi, R.K. / Perband, M. / Betzel, C. / Dey, S. / Sharma, S. / Singh, T.P.
History
DepositionFeb 12, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionMar 10, 2009ID: 1TJQ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Nov 1, 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 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2 VRV-PL-VIIIa
B: PHQ VAL ALA ARG SER peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5035
Polymers14,2152
Non-polymers2883
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.561, 52.561, 47.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Phospholipase A2 VRV-PL-VIIIa / Phosphatidylcholine 2-acylhydrolase / DPLA2 / P1


Mass: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii russellii (snake) / References: UniProt: P59071, phospholipase A2
#2: Protein/peptide PHQ VAL ALA ARG SER peptide


Type: Peptide-like / Class: Inhibitor / Mass: 585.073 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: CARBOBENZOXY-DEHYDRO-VAL-ALA-ARG-SER
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M AMMONIUM SULPHATE, 30% PEG, CaCl2, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.806 / Wavelength: 0.803 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 5, 2003 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8061
20.8031
ReflectionResolution: 1.2→30 Å / Num. all: 35175 / Num. obs: 35175 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 11.8 Å2 / Rsym value: 0.078 / Net I/σ(I): 20.5
Reflection shellResolution: 1.2→1.27 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.487 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SKG

1skg


Resolution: 1.25→29.36 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.917 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.047 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 921 2.6 %RANDOM
Rwork0.187 ---
all0.189 35175 --
obs0.187 35175 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: 12.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.25→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 0 15 199 1198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211015
X-RAY DIFFRACTIONr_bond_other_d0.0020.02857
X-RAY DIFFRACTIONr_angle_refined_deg1.8562.0121352
X-RAY DIFFRACTIONr_angle_other_deg1.03732019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0993116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.20915192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1370.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021062
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02203
X-RAY DIFFRACTIONr_nbd_refined0.4350.3283
X-RAY DIFFRACTIONr_nbd_other0.2240.3814
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.5135
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1480.53
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4830.319
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3780.354
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4760.536
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.661.5614
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2272965
X-RAY DIFFRACTIONr_scbond_it1.4863401
X-RAY DIFFRACTIONr_scangle_it2.3294.5387
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.231 74
Rwork0.235 2587

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