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- PDB-4p27: Structure of Schistosoma mansoni venom allergen-like protein 4 (S... -

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Basic information

Entry
Database: PDB / ID: 4p27
TitleStructure of Schistosoma mansoni venom allergen-like protein 4 (SmVAL4)
ComponentsVenom allergen-like (VAL) 4 protein
KeywordsALLERGEN / Pathogenesis Related Protein / SCP/TAPS
Function / homology
Function and homology information


extracellular space
Similarity search - Function
Venom allergen 5-like / Cysteine-rich secretory protein-related / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Venom allergen-like protein 4
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 2.16 Å
AuthorsAsojo, O.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Schistosoma mansoni venom allergen-like protein 4 (SmVAL4) is a novel lipid-binding SCP/TAPS protein that lacks the prototypical CAP motifs.
Authors: Kelleher, A. / Darwiche, R. / Rezende, W.C. / Farias, L.P. / Leite, L.C. / Schneiter, R. / Asojo, O.A.
History
DepositionMar 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 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: Venom allergen-like (VAL) 4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0642
Polymers18,8431
Non-polymers2211
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.645, 78.645, 83.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Venom allergen-like (VAL) 4 protein / Venom allergen-like protein 4


Mass: 18843.232 Da / Num. of mol.: 1 / Fragment: UNP residues 20-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_002070 / Production host: Pichia (fungus) / References: UniProt: Q1X6L4
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.96 Å3/Da / Density % sol: 68.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.085 M sodium acetate trihydrate at pH 4.6, 25% (w/v) PEG 2000, 0.17 M ammonium sulfate and 15% (v/v) glycerol, 8 mg/ml SmVAL4 in Sodium Citrate at pH 5.0
PH range: 4.6 - 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.518
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray / Wavelength: 1.518
Radiation wavelengthWavelength: 1.518 Å / Relative weight: 1
ReflectionResolution: 2.15→34.05 Å / Num. obs: 15770 / % possible obs: 99.7 % / Redundancy: 21.2 % / Rsym value: 0.071 / Net I/σ(I): 5.1
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 21.2 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1 / Rsym value: 0.693 / % possible all: 99.3

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 2.16→28.63 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.382 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20877 803 5.1 %RANDOM
Rwork0.18039 ---
obs0.18188 14947 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.084 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.16→28.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 14 66 1338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021304
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2531.9661756
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
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_restr0.1590.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211002
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_it4.1073.534619
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.495.264772
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.5584.044685
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.58336.1421726
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: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 54 -
Rwork0.224 1088 -
obs--99.3 %

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