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

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Basic information

Entry
Database: PDB / ID: 4qyo
TitleCrystal Structure of anti-MSP2 Fv fragment (mAb6D8)in complex with MSP2 14-22
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 K1 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.208 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)25,5993
Polymers25,5993
Non-polymers00
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-16 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.941, 60.712, 43.703
Angle α, β, γ (deg.)90.00, 106.68, 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


Mass: 1150.337 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 33-41 / Source method: obtained synthetically / Source: (synth.) Plasmodium falciparum K1 (eukaryote) / References: UniProt: Q03643
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 22% PEG 8000, 0.2M NaCl, 0.1M NaOAc, pH 4.7, 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: Mar 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.208→41.864 Å / Num. all: 62158 / Num. obs: 62158 / % possible obs: 96.75 %
Reflection shellResolution: 1.208→1.251 Å / Mean I/σ(I) obs: 1.5 / Num. unique all: 5342 / % possible all: 83.25

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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: PDB ID 3GM0

3gm0


Resolution: 1.208→41.864 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 17.6 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1696 3042 4.89 %RANDOM
Rwork0.1512 ---
all0.1521 62147 --
obs0.1521 62147 96.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.208→41.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1783 0 0 377 2160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081875
X-RAY DIFFRACTIONf_angle_d1.2452561
X-RAY DIFFRACTIONf_dihedral_angle_d11.916679
X-RAY DIFFRACTIONf_chiral_restr0.082282
X-RAY DIFFRACTIONf_plane_restr0.006335
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2081-1.2270.297990.2712188769
1.227-1.24710.25431170.2744267995
1.2471-1.26870.28051400.2534262195
1.2687-1.29170.24871540.2459262996
1.2917-1.31660.25851350.2308266396
1.3166-1.34340.21951190.2317268496
1.3434-1.37270.2091480.2092263396
1.3727-1.40460.21211360.2076267297
1.4046-1.43970.21431490.1909268697
1.4397-1.47860.17311430.1807264797
1.4786-1.52220.18531580.1746268597
1.5222-1.57130.2071360.1568271398
1.5713-1.62750.17251410.1531275999
1.6275-1.69260.16991480.14822767100
1.6926-1.76960.15991260.1412797100
1.7696-1.86290.17481170.13822777100
1.8629-1.97970.13521730.13322769100
1.9797-2.13250.14651370.1262787100
2.1325-2.34710.16091290.12382804100
2.3471-2.68670.15461400.13452794100
2.6867-3.38470.14761350.12782815100
3.3847-41.88960.1421620.12562837100
Refinement TLS params.Method: refined / Origin x: 19.8775 Å / Origin y: 17.242 Å / Origin z: 33.177 Å
111213212223313233
T0.0563 Å20.0081 Å20.0036 Å2-0.06 Å20.0099 Å2--0.0541 Å2
L0.7458 °20.3517 °20.202 °2-1.0008 °20.2298 °2--0.4035 °2
S-0.0405 Å °0.0529 Å °0.033 Å °-0.0793 Å °0.0225 Å °0.0333 Å °-0.0121 Å °0.0014 Å °0.018 Å °
Refinement TLS groupSelection details: ALL

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