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- PDB-6any: Structure of BmVAL-1 -

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Basic information

Entry
Database: PDB / ID: 6any
TitleStructure of BmVAL-1
ComponentsBm4233, isoform b
KeywordsLIPID TRANSPORT / Venom allergen-like / VAL / Ancylostoma secreted protein / ASP / sperm coating protein / SCP / TAPs / testis specific proteins / Tpx / antigen 5 / Ag5 / pathogenesis related-1 / PR-1 / Sc7 / CAP / cysteine-rich secretory protein / CRISP / venom antigen 5 / Excretory-secretory products / sterol binding
Function / homologyVenom allergen 5-like / Cysteine-rich secretory protein-related / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / : / Bm4233, isoform a / Bm4233, isoform b
Function and homology information
Biological speciesBrugia malayi (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsAsojo, O.A.
CitationJournal: Int. J. Parasitol. / Year: 2018
Title: Crystal structure of Brugia malayi venom allergen-like protein-1 (BmVAL-1), a vaccine candidate for lymphatic filariasis.
Authors: Darwiche, R. / Lugo, F. / Drurey, C. / Varossieau, K. / Smant, G. / Wilbers, R.H.P. / Maizels, R.M. / Schneiter, R. / Asojo, O.A.
History
DepositionAug 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 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: Bm4233, isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5274
Polymers23,3311
Non-polymers1,1963
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.790, 85.790, 66.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsMonomer as determined by native gel electrophoresis

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Components

#1: Protein Bm4233, isoform b / Venom allergen antigen-like protein 1 / Vespid allergen antigen homolog


Mass: 23330.713 Da / Num. of mol.: 1 / Fragment: residues 17-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: Bm4233, BM_Bm4233 / Production host: Nicotiana benthamiana (plant) / References: UniProt: O44932, UniProt: A0A0J9Y762*PLUS
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEGS 2 #67

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→60.66 Å / Num. all: 22409 / Num. obs: 11799 / % possible obs: 96.4 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.03196 / Rpim(I) all: 0.03196 / Rrim(I) all: 0.0452 / Net I/σ(I): 9.7
Reflection shellRmerge(I) obs: 0.1561 / Num. measured obs: 1735 / Num. unique all: 997 / CC1/2: 0.927 / Rpim(I) all: 0.1561 / Rrim(I) all: 0.2207

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
CrystalCleardata collection
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1u53

1u53


Resolution: 2.25→44.87 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.437 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 977 8.3 %RANDOM
Rwork0.18025 ---
obs0.18316 10814 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.949 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 2.25→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 78 175 1883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191741
X-RAY DIFFRACTIONr_bond_other_d0.0030.021574
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.9892354
X-RAY DIFFRACTIONr_angle_other_deg1.10633682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4145205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92123.97478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.27415308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6731513
X-RAY DIFFRACTIONr_chiral_restr0.1130.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021871
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02343
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_it1.6471.814823
X-RAY DIFFRACTIONr_mcbond_other1.6381.812822
X-RAY DIFFRACTIONr_mcangle_it2.3972.7141027
X-RAY DIFFRACTIONr_mcangle_other2.3992.7161028
X-RAY DIFFRACTIONr_scbond_it2.7392.298918
X-RAY DIFFRACTIONr_scbond_other2.7372.292914
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2043.3011322
X-RAY DIFFRACTIONr_long_range_B_refined5.39723.0282041
X-RAY DIFFRACTIONr_long_range_B_other5.29822.7141998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 62 -
Rwork0.205 687 -
obs--83.41 %

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