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- PDB-4qy8: Crystal Structure of anti-MSP2 Fv fragment (mAb6D8) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4qy8
TitleCrystal Structure of anti-MSP2 Fv fragment (mAb6D8) in complex with 3D7-MSP2 14-30
Components
  • Fv fragment(mAb6D8) heavy chain
  • Fv fragment(mAb6D8) light chain
  • Merozoite surface antigen 2
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / N-TERMINAL MSP2 / unstructured antigen
Function / homology
Function and homology information


side of membrane / cell adhesion / plasma membrane
Similarity search - Function
Merozoite surface antigen 2 (MSA-2) / Merozoite Surface Antigen 2 (MSA-2) family / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Merozoite surface protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Plasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.353 Å
AuthorsMorales, R.A.V. / MacRaild, C.A. / Seow, J. / Bankala, K. / Drinkwater, N. / McGowan, S. / Rouet, R. / Christ, D. / Anders, R.F. / Norton, R.S.
CitationJournal: Sci Rep / Year: 2015
Title: Structural basis for epitope masking and strain specificity of a conserved epitope in an intrinsically disordered malaria vaccine candidate.
Authors: Morales, R.A. / MacRaild, C.A. / Seow, J. / Krishnarjuna, B. / Drinkwater, N. / Rouet, R. / Anders, R.F. / Christ, D. / McGowan, S. / Norton, R.S.
History
DepositionJul 24, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 9, 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: Fv fragment(mAb6D8) heavy chain
B: Fv fragment(mAb6D8) light chain
Q: Merozoite surface antigen 2


Theoretical massNumber of molelcules
Total (without water)26,4183
Polymers26,4183
Non-polymers00
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-17 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.107, 60.323, 43.477
Angle α, β, γ (deg.)90.00, 107.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fv fragment(mAb6D8) heavy chain


Mass: 12489.899 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody Fv fragment(mAb6D8) light chain


Mass: 11959.071 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide Merozoite surface antigen 2 / MEROZOITE SURFACE PROTEIN 2 / MSA-2 / 45 kDa merozoite surface antigen


Mass: 1969.252 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 33-49 / Source method: obtained synthetically / Source: (synth.) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: P50498
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 30% PEG 8000, 0.2M NaCl, 0.1M NaOAc, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.35→34.39 Å / Num. all: 44204 / Num. obs: 44204 / % possible obs: 97.4 %
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.1 / % possible all: 95.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QYO

4qyo


Resolution: 1.353→34.23 Å / SU ML: 0.12 / σ(F): 1.35 / Phase error: 17.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1647 2247 5.08 %
Rwork0.1518 --
obs0.1525 44199 97.27 %
all-44204 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.353→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 0 369 2192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051875
X-RAY DIFFRACTIONf_angle_d1.12547
X-RAY DIFFRACTIONf_dihedral_angle_d11.746673
X-RAY DIFFRACTIONf_chiral_restr0.069279
X-RAY DIFFRACTIONf_plane_restr0.004332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3526-1.3820.25691330.25222517X-RAY DIFFRACTION94
1.382-1.41410.27191220.2462604X-RAY DIFFRACTION96
1.4141-1.44950.30161270.23312599X-RAY DIFFRACTION96
1.4495-1.48870.24671190.21052602X-RAY DIFFRACTION97
1.4887-1.53250.2291200.19632599X-RAY DIFFRACTION97
1.5325-1.5820.18481370.19142608X-RAY DIFFRACTION97
1.582-1.63850.2331360.17452629X-RAY DIFFRACTION97
1.6385-1.70410.17941350.1692616X-RAY DIFFRACTION97
1.7041-1.78170.18551450.15642592X-RAY DIFFRACTION97
1.7817-1.87560.15831570.15482625X-RAY DIFFRACTION98
1.8756-1.99310.16651330.13732650X-RAY DIFFRACTION98
1.9931-2.1470.14351550.13742619X-RAY DIFFRACTION98
2.147-2.3630.13941650.13182635X-RAY DIFFRACTION99
2.363-2.70480.17441610.13932650X-RAY DIFFRACTION99
2.7048-3.40720.1441410.13282696X-RAY DIFFRACTION99
3.4072-34.24060.13371610.13122711X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 19.5541 Å / Origin y: 16.9193 Å / Origin z: 32.9832 Å
111213212223313233
T0.0701 Å20.0128 Å20.0051 Å2-0.0781 Å20.018 Å2--0.0664 Å2
L0.7822 °20.2759 °20.3319 °2-1.1552 °20.4921 °2--0.6905 °2
S-0.05 Å °0.053 Å °0.0286 Å °-0.0482 Å °0.0451 Å °0.0517 Å °-0.0088 Å °0.0552 Å °0.0025 Å °
Refinement TLS groupSelection details: all

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