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- PDB-2j4w: Structure of a Plasmodium vivax apical membrane antigen 1-Fab F8.... -

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Basic information

Entry
Database: PDB / ID: 2j4w
TitleStructure of a Plasmodium vivax apical membrane antigen 1-Fab F8.12.19 complex
Components
  • (FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19) x 2
  • APICAL MEMBRANE ANTIGEN 1
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN DOMAIN / IMMUNOGLOBULIN C REGION / MEMBRANE / TRANSMEMBRANE / HYPOTHETICAL PROTEIN / ANTIBODY CROSS-REACTIVITY / SURFACE ACTIVE PROTEIN / MALARIA VACCINE CANDIDATE / APICAL MEMBRANE ANTIGEN 1
Function / homology
Function and homology information


Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site ...Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ighg protein / Ig-like domain-containing protein / Apical membrane antigen 1
Similarity search - Component
Biological speciesPLASMODIUM VIVAX (malaria parasite P. vivax)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsIgonet, S. / Vulliez-Le Normand, B. / Faure, G. / Riottot, M.M. / Kocken, C.H.M. / Thomas, A.W. / Bentley, G.A.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Cross-Reactivity Studies of an Anti-Plasmodium Vivax Apical Membrane Antigen 1 Monoclonal Antibody: Binding and Structural Characterisation.
Authors: Igonet, S. / Vulliez-Le Normand, B. / Faure, G. / Riottot, M.M. / Kocken, C.H.M. / Thomas, A.W. / Bentley, G.A.
History
DepositionSep 7, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 11, 2020Group: Derived calculations / Other / Polymer sequence / Category: entity_poly / pdbx_database_status / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Mar 18, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count ..._pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 2.2Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: APICAL MEMBRANE ANTIGEN 1
H: FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19
L: FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19


Theoretical massNumber of molelcules
Total (without water)98,8373
Polymers98,8373
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-32 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.787, 171.787, 44.748
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein APICAL MEMBRANE ANTIGEN 1 / PLASMODIUM VIVAX APICAL MEMBRANE ANTIGEN 1


Mass: 51361.934 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM VIVAX (malaria parasite P. vivax)
Strain: SAL I / Plasmid: PHIL-S1 / Production host: PICHIA PASTORIS (fungus) / References: UniProt: Q9TY14
#2: Antibody FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19 / ANTIGEN-BINDING FRAGMENT FAB / HEAVY CHAIN


Mass: 24189.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MONOCLONAL ANTIBODY ISOTYPE IS IGG1, KAPPA / Source: (natural) MUS MUSCULUS (house mouse) / Strain: BALB/C / References: UniProt: Q569B4*PLUS
#3: Antibody FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19 / ANTIGEN-BINDING FRAGMENT FAB / LIGHT CHAIN


Mass: 23285.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MONOCLONAL ANTIBODY ISOTYPE IS IGG1, KAPPA / Source: (natural) MUS MUSCULUS (house mouse) / Strain: BALB/C / References: UniProt: Q5XFY8*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN D, SER 136 TO ASN ENGINEERED RESIDUE IN CHAIN D, ASN 184 TO ASP ...ENGINEERED RESIDUE IN CHAIN D, SER 136 TO ASN ENGINEERED RESIDUE IN CHAIN D, ASN 184 TO ASP ENGINEERED RESIDUE IN CHAIN D, ASN 399 TO GLU
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: 3.61 Å3/Da / Density % sol: 65.63 %
Crystal growpH: 4.4
Details: PVAMA1 AND FAB-F8.12.19 WERE MIXED IN A 1:1 STOICHIOMETRIC RATIO AND LEFT TO INCUBATE FOR 4 HOURS AT ROOM TEMPERATURE TO FORM THE ANTIBODY-ANTIGEN COMPLEX BEFORE MIXING WITH CRYSTALLISATION ...Details: PVAMA1 AND FAB-F8.12.19 WERE MIXED IN A 1:1 STOICHIOMETRIC RATIO AND LEFT TO INCUBATE FOR 4 HOURS AT ROOM TEMPERATURE TO FORM THE ANTIBODY-ANTIGEN COMPLEX BEFORE MIXING WITH CRYSTALLISATION SCREENING BUFFERS. CRYSTALS USED FOR DIFFRACTION MEASUREMENTS WERE OBTAINED AS FOLLOWS. THE CRYSTALLISATION BUFFER IN THE RESERVOIR COMPRISED 10% PEG 6000 AND 0.1 M SODIUM ACETATE BUFFERED TO PH 4.4. THE CRYSTALLISATION DROP WAS PREPARED BY ADDING 0.8 MICROLITRES OF THE CRYSTALLISATION BUFFER TO 0.8 MICROLITRES OF THE PVAMA1-FAB COMPLEX, GIVING A FINAL PROTEIN CONCENTRATION OF 3.9 MG/ML.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 26533 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.8
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.93 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2IGF, 1W8K

2igf

1w8k


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.612 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FAB LIGHT AND HEAVY CHAINS ARE NUMBERED ACCORDING TO THE KABAT CONVENTION. ANTIGEN RESIDUES D43 TO D420 AND RESIDUES D455 TO D487 ARE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FAB LIGHT AND HEAVY CHAINS ARE NUMBERED ACCORDING TO THE KABAT CONVENTION. ANTIGEN RESIDUES D43 TO D420 AND RESIDUES D455 TO D487 ARE DISSORDERED IN THE CRYSTAL STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1335 5.1 %RANDOM
Rwork0.187 ---
obs0.19 24858 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.31 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å2-1.28 Å20 Å2
2---2.57 Å20 Å2
3---3.85 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3606 0 0 155 3761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223717
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8931.955063
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4165469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55823.986148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.32515589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8521517
X-RAY DIFFRACTIONr_chiral_restr0.1250.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022817
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.21515
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22482
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2195
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.50422406
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.62233832
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5473.51513
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.50841231
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: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.391 94
Rwork0.311 1558

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