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- PDB-1m8t: Structure of an acidic Phospholipase A2 from the venom of Ophioph... -

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Basic information

Entry
Database: PDB / ID: 1m8t
TitleStructure of an acidic Phospholipase A2 from the venom of Ophiophagus hannah at 2.1 resolution from a hemihedrally twinned crystal form
ComponentsPhospholipase a2
KeywordsHYDROLASE / phospholipase a2 structure / twinned crystal / alpha / beta
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / phospholipid metabolic process / phospholipid binding / positive regulation of fibroblast proliferation / fatty acid biosynthetic process / toxin activity / signaling receptor binding ...phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / phospholipid metabolic process / phospholipid binding / positive regulation of fibroblast proliferation / fatty acid biosynthetic process / toxin activity / signaling receptor 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 / 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
HEXANE-1,6-DIOL / Acidic phospholipase A2 2
Similarity search - Component
Biological speciesOphiophagus hannah (king cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXu, S. / Gu, L. / Wang, Q. / Shu, Y. / Lin, Z.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of a king cobra phospholipase A2 determined from a hemihedrally twinned crystal.
Authors: Xu, S. / Gu, L. / Wang, Q. / Shu, Y. / Song, S. / Lin, Z.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Preliminary crystallographic study of an acidic phospholipase A2 from Ophiophagus hannah (king cobra)
Authors: Xu, S. / Gu, L. / Wang, Q. / Shu, Y. / Lin, Z.
History
DepositionJul 26, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / 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.ptnr2_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _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 1.4Oct 30, 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
B: Phospholipase a2
C: Phospholipase a2
D: Phospholipase a2
E: Phospholipase a2
F: Phospholipase a2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,62622
Polymers79,2046
Non-polymers1,42216
Water15,403855
1
A: Phospholipase a2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7136
Polymers13,2011
Non-polymers5135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phospholipase a2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3593
Polymers13,2011
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phospholipase a2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4774
Polymers13,2011
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phospholipase a2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5955
Polymers13,2011
Non-polymers3954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Phospholipase a2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2412
Polymers13,2011
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Phospholipase a2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2412
Polymers13,2011
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.06, 98.06, 132.39
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Phospholipase a2


Mass: 13200.592 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Ophiophagus hannah (king cobra) / Secretion: venom / References: UniProt: Q9DF33, phospholipase A2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 855 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 3.4M 1,6-hexanediol, 0.2M magnesium chloride, 0.1M tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
23.4 M1,6-hexanediol1drop
30.2 M1dropMgCl2
40.1 MTris-HCl1droppH8.5
50.1 MTris-HCl1reservoirpH8.5
66 M1,6-hexanediol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jan 23, 2002 / Details: Osmic Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→17 Å / Num. all: 41966 / Num. obs: 41966 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 16.1 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 38.1
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 14 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 7.4 / Num. unique all: 4153 / % possible all: 98.8
Reflection
*PLUS
Lowest resolution: 17 Å / Num. measured all: 1527037
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 98.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1POA

1poa


Resolution: 2.1→16.99 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: TWINNED R VALUE (WORKING SET): 0.195, TWINNED FREE R VALUE: 0.215; TWINNED BIN R VALUE (WORKING SET): 0.285, TWINNED BIN FREE R VALUE: 0.248
RfactorNum. reflection% reflection
Rfree0.213 2026 4.8 %
Rwork0.192 --
all0.196 41938 -
obs-41938 99.9 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 95.581 Å2 / ksol: 0.352776 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.98 Å21.14 Å20 Å2
2---3.98 Å20 Å2
3---7.97 Å2
Refinement stepCycle: LAST / Resolution: 2.1→16.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5473 0 86 855 6414
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it1.492
X-RAY DIFFRACTIONc_scangle_it2.242.5
LS refinement shellResolution: 2.1→2.23 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 347 5 %
Rwork0.237 --
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4BBO.PARAMBBO.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 17 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.47
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87

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