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- PDB-5xaj: Structural mimicry of the dengue virus envelope glycoprotein reve... -

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Basic information

Entry
Database: PDB / ID: 5xaj
TitleStructural mimicry of the dengue virus envelope glycoprotein revealed by the crystallographic study of an idiotype-anti-idiotype Fab complex.
Components
  • (Fab E1 heavy ...) x 2
  • Fab E1 light chain
  • FabHM14c10 heavy chain
  • FabHM14c10 light chain
KeywordsIMMUNE SYSTEM / Complex / Antibody / Anti-idiotype
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWong, Y.H. / Goh, B.C. / Lescar, J.
Funding support Singapore, 3items
OrganizationGrant numberCountry
MOERG62/12 Singapore
NMRCNMRC/CBRG/0028/2014 Singapore
SMARTSMART Scholarship Singapore
CitationJournal: J. Virol. / Year: 2017
Title: Structural mimicry of the dengue virus envelope glycoprotein revealed by the crystallographic study of an idiotype-anti-idiotype Fab complex
Authors: Wong, Y.H. / Goh, B.C. / Lim, S.Y. / Teo, E.W. / Lim, A.P.C. / Dedon, P.C. / Hanson, B.J. / MacAry, P.A. / Lescar, J.
History
DepositionMar 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FabHM14c10 heavy chain
B: FabHM14c10 light chain
C: Fab E1 light chain
D: Fab E1 light chain
E: Fab E1 heavy chain
F: Fab E1 heavy chain
H: FabHM14c10 heavy chain
L: FabHM14c10 light chain


Theoretical massNumber of molelcules
Total (without water)186,0298
Polymers186,0298
Non-polymers00
Water23,2931293
1
A: FabHM14c10 heavy chain
B: FabHM14c10 light chain


Theoretical massNumber of molelcules
Total (without water)47,4522
Polymers47,4522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-29 kcal/mol
Surface area19980 Å2
MethodPISA
2
C: Fab E1 light chain
E: Fab E1 heavy chain


Theoretical massNumber of molelcules
Total (without water)45,4032
Polymers45,4032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-23 kcal/mol
Surface area20640 Å2
MethodPISA
3
D: Fab E1 light chain
F: Fab E1 heavy chain
L: FabHM14c10 light chain


Theoretical massNumber of molelcules
Total (without water)69,1773
Polymers69,1773
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-23 kcal/mol
Surface area20520 Å2
MethodPISA
4
H: FabHM14c10 heavy chain


Theoretical massNumber of molelcules
Total (without water)23,9971
Polymers23,9971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-27 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.300, 47.590, 220.759
Angle α, β, γ (deg.)90.00, 93.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 5 types, 8 molecules AHBLCDEF

#1: Antibody FabHM14c10 heavy chain


Mass: 23997.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: ESCHERICHIA COLI (E. coli)
#2: Antibody FabHM14c10 light chain


Mass: 23455.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: ESCHERICHIA COLI (E. coli)
#3: Antibody Fab E1 light chain


Mass: 22948.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: ESCHERICHIA COLI (E. coli)
#4: Antibody Fab E1 heavy chain


Mass: 22454.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: ESCHERICHIA COLI (E. coli)
#5: Antibody Fab E1 heavy chain


Mass: 22773.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: ESCHERICHIA COLI (E. coli)

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Non-polymers , 1 types, 1293 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1293 / 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: 3.29 Å3/Da / Density % sol: 62.57 % / Description: Plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Ammonium acetate, Bis Tris Propane pH 5.5, PEG 10,000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.0428 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0428 Å / Relative weight: 1
ReflectionResolution: 2.5→52.67 Å / Num. obs: 84640 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 45.15 Å2 / Net I/σ(I): 6.5
Reflection shellResolution: 2.5→2.64 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 12224 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.93 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.893 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.335 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.38 / SU Rfree Blow DPI: 0.252 / SU Rfree Cruickshank DPI: 0.246
RfactorNum. reflection% reflectionSelection details
Rfree0.239 4183 4.94 %RANDOM
Rwork0.185 ---
obs0.187 84627 99.7 %-
Displacement parametersBiso mean: 36.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.8733 Å20 Å2-1.2126 Å2
2---4.4598 Å20 Å2
3---6.3331 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: 1 / Resolution: 2.5→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13020 0 0 1311 14331
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113354HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2818203HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4333SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes261HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1963HARMONIC5
X-RAY DIFFRACTIONt_it13354HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.69
X-RAY DIFFRACTIONt_other_torsion19.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1762SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14710SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 312 5.09 %
Rwork0.226 5817 -
all0.23 6129 -
obs--99.71 %

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