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- PDB-2qhd: Crystal structure of ecarpholin S (ser49-PLA2) complexed with fat... -

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Basic information

Entry
Database: PDB / ID: 2qhd
TitleCrystal structure of ecarpholin S (ser49-PLA2) complexed with fatty acid
ComponentsPhospholipase A2
KeywordsHYDROLASE / BETA SHEET / THREE HELICES / PROTEIN-LIGAND COMPLEX
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / 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
LAURIC ACID / Basic phospholipase A2 homolog ecarpholin S
Similarity search - Component
Biological speciesEchis carinatus (saw-scaled viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZhou, X. / Tan, T.C. / Valiyaveettil, S. / Go, M.L. / Kini, R.M. / Sivaraman, J.
CitationJournal: Biophys.J. / Year: 2008
Title: Structural Characterization of Myotoxic Ecarpholin S from Echis carinatus Venom
Authors: Zhou, X. / Tan, T.C. / Valiyaveettil, S. / Go, M.L. / Kini, R.M. / Velazquez-Campoy, A. / Sivaraman, J.
History
DepositionJul 2, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)28,0784
Polymers27,6782
Non-polymers4012
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.096, 62.096, 124.252
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.9999, -0.0112, 0.0031), (0.0108, -0.7932, 0.6089), (-0.0044, 0.6089, 0.7932)174.4428, -1.514, 0.7045

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Components

#1: Protein Phospholipase A2 / Ecarpholin S/lauric acid complex / Phosphatidylcholine 2-acylhydrolase


Mass: 13838.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: snake venom gland / Source: (natural) Echis carinatus (saw-scaled viper) / References: UniProt: P48650, phospholipase A2
#2: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5
Details: 2M ammonium sulfate, 0.1M Tris-HCl pH8.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 30306 / % possible obs: 96.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.08 / Χ2: 1.784 / Net I/σ(I): 20.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.763.80.32126921.28387.1
1.76-1.835.80.23329820.34297.9
1.83-1.915.70.70129244.96695
1.91-2.026.40.55230103.95196.8
2.02-2.147.40.2130412.31598.4
2.14-2.317.70.40730232.70297.5
2.31-2.549.10.05230711.01499
2.54-2.919.20.05631070.93499.2
2.91-3.669.30.04131660.97799.4
3.66-509.70.02832901.04498.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation4 Å30.12 Å
Translation4 Å30.12 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QHE

2qhe


Resolution: 1.95→30 Å / FOM work R set: 0.825 / σ(F): 838
RfactorNum. reflection% reflection
Rfree0.268 1957 9.4 %
Rwork0.228 --
obs-19796 94.7 %
Solvent computationBsol: 41.88 Å2
Displacement parametersBiso mean: 29.154 Å2
Baniso -1Baniso -2Baniso -3
1--3.509 Å2-2.253 Å20 Å2
2---3.509 Å20 Å2
3---7.019 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1918 0 28 243 2189
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.296
X-RAY DIFFRACTIONc_mcbond_it1.3821.5
X-RAY DIFFRACTIONc_scbond_it2.1852
X-RAY DIFFRACTIONc_mcangle_it2.0482
X-RAY DIFFRACTIONc_scangle_it3.1852.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 39

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.95-1.970.243410.238382423
1.97-1.980.333420.221395437
1.98-20.298530.208413466
2-2.020.258480.216378426
2.02-2.040.255440.246405449
2.04-2.060.325360.228434470
2.06-2.080.416510.34500551
2.08-2.110.241510.236402453
2.11-2.130.227490.218441490
2.13-2.150.236530.211444497
2.15-2.180.212450.198434479
2.18-2.20.27600.223435495
2.2-2.230.262360.226405441
2.23-2.260.482510.493475526
2.26-2.290.267420.25419461
2.29-2.330.308560.222441497
2.33-2.360.323540.22446500
2.36-2.40.342480.237481529
2.4-2.440.336520.237451503
2.44-2.480.285460.244464510
2.48-2.520.273510.213449500
2.52-2.570.333620.207479541
2.57-2.620.279360.234457493
2.62-2.680.293600.253479539
2.68-2.740.282500.246458508
2.74-2.810.294540.258464518
2.81-2.890.277650.235456521
2.89-2.970.333490.25490539
2.97-3.070.304550.248479534
3.07-3.180.364530.249470523
3.18-3.310.296480.254504552
3.31-3.460.215440.223492536
3.46-3.640.212590.207480539
3.64-3.860.227610.183482543
3.86-4.160.219430.188488531
4.16-4.580.221530.181508561
4.58-5.240.195530.188499552
5.24-6.590.225520.213520572
6.59-300.219510.206540591
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5lau.paramlau.top

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