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- PDB-1s6b: X-ray Crystal Structure of a Complex Formed Between Two Homologou... -

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Basic information

Entry
Database: PDB / ID: 1s6b
TitleX-ray Crystal Structure of a Complex Formed Between Two Homologous Isoforms of Phospholipase A2 from Naja naja sagittifera: Principle of Molecular Association and Inactivation
Components(Phospholipase A2 isoform ...) x 2
KeywordsHYDROLASE / Phospholipase A2 / molecular conformation / enzyme activity
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 / 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
ACETIC ACID / PHOSPHATE ION / Basic phospholipase A2 1 / Acidic phospholipase A2 2
Similarity search - Component
Biological speciesNaja sagittifera (cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJabeen, T. / Sharma, S. / Singh, R.K. / Kaur, P. / Singh, T.P.
Citation
Journal: Proteins / Year: 2005
Title: Crystal structure of a calcium-induced dimer of two isoforms of cobra phospholipase A2 at 1.6 A resolution.
Authors: Jabeen, T. / Sharma, S. / Singh, N. / Singh, R.K. / Kaur, P. / Perbandt, M. / Betzel, C.h. / Srinivasan, A. / Singh, T.P.
#1: Journal: To be Published
Title: Crystal Structure of an Acidic Phospholipase A2 from Naja Naja Sagittifera at 1.5 A Resolution
Authors: Singh, R.K. / Sharma, S. / Jabeen, T. / Kaur, P. / Singh, T.P.
History
DepositionJan 23, 2004Deposition site: RCSB / Processing site: PDBJ
SupersessionFeb 10, 2004ID: 1LFJ
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
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 / 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 / _diffrn_source.pdbx_synchrotron_site / _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 1.5Nov 13, 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 isoform 1
B: Phospholipase A2 isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9008
Polymers26,5092
Non-polymers3906
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-38 kcal/mol
Surface area11380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.537, 64.537, 57.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Phospholipase A2 isoform ... , 2 types, 2 molecules AB

#1: Protein Phospholipase A2 isoform 1 / Phospholipase A2 / Phosphatidylcholine 2-acylhydrolase


Mass: 13220.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja sagittifera (cobra) / Secretion: venom / References: UniProt: P60043, phospholipase A2
#2: Protein Phospholipase A2 isoform 2 / Phospholipase A2 / Phosphatidylcholine 2-acylhydrolase


Mass: 13288.681 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja sagittifera (cobra) / Secretion: venom / References: UniProt: P60044, phospholipase A2

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Non-polymers , 4 types, 360 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: calcium chloride, tris, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMsodium phosphate1drop
220 mMcalcium acetate1drop
315 mg/mlprotein1drop
425 %ethanol1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.802 / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 11, 2001 / Details: MIRRORS
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8021
20.911
ReflectionResolution: 1.6→20 Å / Num. obs: 27946 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 17.9 % / Biso Wilson estimate: 29.1 Å2 / Rsym value: 0.043 / Net I/σ(I): 26
Reflection shellResolution: 1.6→1.68 Å / Mean I/σ(I) obs: 3.02 / Rsym value: 0.329 / % possible all: 97.3
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Num. measured all: 500751 / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 97.3 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PSH

1psh


Resolution: 1.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: USED CONJUGATE DIRECTION METHOD
RfactorNum. reflection% reflectionSelection details
Rfree0.236 730 0.025 %RANDOM
Rwork0.206 ---
all0.212 27946 --
obs0.212 27946 98.6 %-
Displacement parametersBiso mean: 30.8 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1837 0 12 363 2212
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d0.033
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.1
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg16.96

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