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- PDB-4dcf: Structure of MTX-II from Bothrops brazili -

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Basic information

Entry
Database: PDB / ID: 4dcf
TitleStructure of MTX-II from Bothrops brazili
ComponentsMTX-II chain A
KeywordsHYDROLASE / Lys49 Phospholipase / phospholipase
Function / homology
Function and homology information


calcium-dependent phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / 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
Basic phospholipase A2 homolog 2
Similarity search - Component
Biological speciesBothrops brazili (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsUllah, A. / Souza, T.A.C.B. / Betzel, C. / Murakami, M.T. / Arni, R.K.
CitationJournal: Int.J.Biol.Macromol. / Year: 2012
Title: Crystallographic portrayal of different conformational states of a Lys49 phospholipase A2 homologue: insights into structural determinants for myotoxicity and dimeric configuration.
Authors: Ullah, A. / Souza, T.A. / Betzel, C. / Murakami, M.T. / Arni, R.K.
History
DepositionJan 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Sep 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MTX-II chain A
B: MTX-II chain A
C: MTX-II chain A
D: MTX-II chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8936
Polymers55,5054
Non-polymers3882
Water1,838102
1
A: MTX-II chain A
B: MTX-II chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1414
Polymers27,7522
Non-polymers3882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: MTX-II chain A
D: MTX-II chain A


Theoretical massNumber of molelcules
Total (without water)27,7522
Polymers27,7522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.400, 128.886, 67.008
Angle α, β, γ (deg.)90.00, 105.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
MTX-II chain A


Mass: 13876.159 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bothrops brazili (snake) / References: UniProt: I6L8L6*PLUS
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.22 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.1 M tris pH 8.2, 25% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 13286 / Num. obs: 12516 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.116
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2.68 / Num. unique all: 1132 / % possible all: 86.1

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2H8I

2h8i


Resolution: 2.7→19.72 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.808 / SU B: 22.661 / SU ML: 0.448 / Cross valid method: THROUGHOUT / ESU R Free: 0.519 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31981 629 5 %RANDOM
Rwork0.22267 ---
obs0.2276 11881 93.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.954 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.16 Å2
2--0.04 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3837 0 26 102 3965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223965
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.995323
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9265486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.07724.601163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.17615768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3451520
X-RAY DIFFRACTIONr_chiral_restr0.10.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212892
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5311.52434
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06323902
X-RAY DIFFRACTIONr_scbond_it1.39631531
X-RAY DIFFRACTIONr_scangle_it2.4124.51421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 30 -
Rwork0.306 757 -
obs--82.84 %

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