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- PDB-2g58: Crystal structure of a complex of phospholipase A2 with a designe... -

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Basic information

Entry
Database: PDB / ID: 2g58
TitleCrystal structure of a complex of phospholipase A2 with a designed peptide inhibitor Dehydro-Ile-Ala-Arg-Ser at 0.98 A resolution
Components
  • (PHQ)IARS
  • Phospholipase A2 VRV-PL-VIIIa
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Phospholipase A2 / dIARS / HYDROLASE-HYDROLASE INHIBITOR complex
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
DEHYDRO-ILE-ALA-ARG-SER / Basic phospholipase A2 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii pulchella (snake)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsPrem Kumar, R. / Singh, N. / Somvanshi, R.K. / Ethayathulla, A.S. / Dey, S. / Sharma, S. / Kaur, P. / Perbandt, M. / Betzel, C. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of a complex of phospholipase A2 with a designed peptide inhibitor Dehydro-Ile-Ala-Arg-Ser at 0.98 A resolution
Authors: Prem Kumar, R. / Singh, N. / Somvanshi, R.K. / Ethayathulla, A.S. / Dey, S. / Sharma, S. / Kaur, P. / Perbandt, M. / Betzel, C. / Singh, T.P.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 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 / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Derived calculations / Source and taxonomy / Category: pdbx_entity_src_syn / struct_conn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific

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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)IARS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5175
Polymers14,2292
Non-polymers2883
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.588, 52.588, 47.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsThe biological Unit is Monomer

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Components

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


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


Type: Peptide-like / Class: Inhibitor / Mass: 599.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) synthetic construct (others) / References: DEHYDRO-ILE-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.: 278 / 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: 2.5 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.2M AMMONIUM SULPHATE, 50% PEG, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 203 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.803 / Wavelength: 0.803 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 30, 2003 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 0.98→20 Å / Num. all: 70330 / Num. obs: 70330 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.2 % / Rsym value: 0.053 / Net I/σ(I): 0.157
Reflection shellResolution: 0.98→1 Å / Mean I/σ(I) obs: 0.024 / Rsym value: 0.473 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZWP

1zwp


Resolution: 0.98→20 Å / Num. parameters: 12647 / Num. restraintsaints: 16246 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1573 1390 2 %RANDOM
Rwork0.133 ---
all-70330 --
obs-69494 93 %-
Displacement parametersBiso mean: 15.1 Å2
Refine analyzeNum. disordered residues: 24 / Occupancy sum hydrogen: 924 / Occupancy sum non hydrogen: 1266
Refinement stepCycle: LAST / Resolution: 0.98→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 0 15 278 1277
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.032
X-RAY DIFFRACTIONs_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.104
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.113
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.051
X-RAY DIFFRACTIONs_approx_iso_adps0.093

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