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- PDB-1umv: Crystal structure of an acidic, non-myotoxic phospholipase A2 fro... -

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Basic information

Entry
Database: PDB / ID: 1umv
TitleCrystal structure of an acidic, non-myotoxic phospholipase A2 from the venom of Bothrops jararacussu
ComponentsHYPOTENSIVE PHOSPHOLIPASE A2
KeywordsLIPASE / ACIDIC / NON-MYOTOXIC / PLA2 / BOTHROPS JARARACUSSU
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / phospholipid binding / regulation of blood pressure / toxin activity / defense response to bacterium / 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
Acidic phospholipase A2 BthA-1
Similarity search - Component
Biological speciesBOTHROPS JARARACUSSU (jararacussu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsMurakami, M.T. / Watanabe, L. / Cintra, A.C.O. / Arni, R.K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Crystal Structure of an Acidic Platelet Aggregation Inhibitor and Hypotensive Phospholipase A(2) in the Monomeric and Dimeric States: Insights Into its Oligomeric State
Authors: Magro, A.J. / Murakami, M.T. / Marcussi, S. / Soares, A.M. / Arni, R.K. / Fontes, M.R.
History
DepositionAug 28, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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
Revision 1.4Nov 20, 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
X: HYPOTENSIVE PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7392
Polymers13,6981
Non-polymers401
Water2,594144
1
X: HYPOTENSIVE PHOSPHOLIPASE A2
hetero molecules

X: HYPOTENSIVE PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4774
Polymers27,3972
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)39.990, 53.990, 90.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein HYPOTENSIVE PHOSPHOLIPASE A2 / PHOSPHOLIPASE A2 / PLA2


Mass: 13698.481 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOTHROPS JARARACUSSU (jararacussu) / Secretion: VENOM / References: UniProt: Q8AXY1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 1.78 Å3/Da / Density % sol: 30.98 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal grow
*PLUS
pH: 4.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Msodium acetate11pH4.6
228 %PEG400011
310 mg/mlprotein12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.537
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.537 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 9034 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 22.1
Reflection shellResolution: 1.79→1.83 Å / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 6 / % possible all: 80.1
Reflection
*PLUS
Highest resolution: 1.79 Å / Lowest resolution: 30 Å / % possible obs: 94.3 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Lowest resolution: 1.84 Å / % possible obs: 80.1 % / Redundancy: 1.2 % / Num. unique obs: 507 / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GOD

1god


Resolution: 1.79→30.29 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.115 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 429 4.8 %RANDOM
Rwork0.161 ---
obs0.164 8580 94.4 %-
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: 16.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.79→30.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 1 144 1094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021978
X-RAY DIFFRACTIONr_bond_other_d0.0010.02790
X-RAY DIFFRACTIONr_angle_refined_deg2.0481.9521322
X-RAY DIFFRACTIONr_angle_other_deg1.01731868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1365121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1480.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021104
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02201
X-RAY DIFFRACTIONr_nbd_refined0.2380.3247
X-RAY DIFFRACTIONr_nbd_other0.270.3982
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1060.5527
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.5144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.319
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.368
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.532
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7162599
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6593958
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8582379
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8243364
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.84 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 18
Rwork0.199 556
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.9
LS refinement shell
*PLUS
Rfactor Rfree: 0.338 / Rfactor Rwork: 0.246

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