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- PDB-5tbd: Crystal Structure of anti-MSP2 Fv fragment (mAb4D11) in complex w... -

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Basic information

Entry
Database: PDB / ID: 5tbd
TitleCrystal Structure of anti-MSP2 Fv fragment (mAb4D11) in complex with 3D7-MSP2 215-222
Components
  • (Fv fragment (mAb4D1) heavy chain) x 2
  • Merozoite surface protein 2
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / C-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: 2.2 Å
AuthorsSeow, J. / Morales, R.A.V. / MacRaild, C.A. / Bankala, K. / Drinkwater, N. / Dingjan, T. / Jaipuria, G. / Wilde, K. / Anders, R.F. / Atreya, H.S. ...Seow, J. / Morales, R.A.V. / MacRaild, C.A. / Bankala, K. / Drinkwater, N. / Dingjan, T. / Jaipuria, G. / Wilde, K. / Anders, R.F. / Atreya, H.S. / Christ, D. / McGowan, S. / Norton, R.S.
Funding support Australia, 2items
OrganizationGrant numberCountry
Indo-Australian Biotechnology fundBF050053 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1042520 Australia
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Structure and Characterisation of a Key Epitope in the Conserved C-Terminal Domain of the Malaria Vaccine Candidate MSP2.
Authors: Seow, J. / Morales, R.A. / MacRaild, C.A. / Krishnarjuna, B. / McGowan, S. / Dingjan, T. / Jaipuria, G. / Rouet, R. / Wilde, K.L. / Atreya, H.S. / Richards, J.S. / Anders, R.F. / Christ, D. ...Authors: Seow, J. / Morales, R.A. / MacRaild, C.A. / Krishnarjuna, B. / McGowan, S. / Dingjan, T. / Jaipuria, G. / Rouet, R. / Wilde, K.L. / Atreya, H.S. / Richards, J.S. / Anders, R.F. / Christ, D. / Drinkwater, N. / Norton, R.S.
History
DepositionSep 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Mar 29, 2017Group: Data collection / Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Fv fragment (mAb4D1) heavy chain
F: Fv fragment (mAb4D1) heavy chain
I: Merozoite surface protein 2
A: Fv fragment (mAb4D1) heavy chain
B: Fv fragment (mAb4D1) heavy chain
C: Merozoite surface protein 2
D: Fv fragment (mAb4D1) heavy chain
G: Fv fragment (mAb4D1) heavy chain
H: Merozoite surface protein 2
J: Fv fragment (mAb4D1) heavy chain
K: Fv fragment (mAb4D1) heavy chain
L: Merozoite surface protein 2


Theoretical massNumber of molelcules
Total (without water)101,88612
Polymers101,88612
Non-polymers00
Water6,575365
1
E: Fv fragment (mAb4D1) heavy chain
F: Fv fragment (mAb4D1) heavy chain
I: Merozoite surface protein 2


Theoretical massNumber of molelcules
Total (without water)25,4723
Polymers25,4723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-12 kcal/mol
Surface area10290 Å2
MethodPISA
2
A: Fv fragment (mAb4D1) heavy chain
B: Fv fragment (mAb4D1) heavy chain
C: Merozoite surface protein 2


Theoretical massNumber of molelcules
Total (without water)25,4723
Polymers25,4723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-12 kcal/mol
Surface area10480 Å2
MethodPISA
3
D: Fv fragment (mAb4D1) heavy chain
G: Fv fragment (mAb4D1) heavy chain
H: Merozoite surface protein 2


Theoretical massNumber of molelcules
Total (without water)25,4723
Polymers25,4723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-12 kcal/mol
Surface area10550 Å2
MethodPISA
4
J: Fv fragment (mAb4D1) heavy chain
K: Fv fragment (mAb4D1) heavy chain
L: Merozoite surface protein 2


Theoretical massNumber of molelcules
Total (without water)25,4723
Polymers25,4723
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-11 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.975, 72.970, 81.965
Angle α, β, γ (deg.)68.19, 78.75, 73.83
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
Fv fragment (mAb4D1) heavy chain


Mass: 12444.808 Da / Num. of mol.: 4
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 (mAb4D1) heavy chain


Mass: 12195.837 Da / Num. of mol.: 4
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 protein 2


Mass: 830.910 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: P50498*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 23% (w/v) PEG3350 0.1 M BIS TRIS (pH 6.0) 0.2 M MgCl2

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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: Aug 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→32.05 Å / Num. obs: 4359 / % possible obs: 100 % / Observed criterion σ(F): 2.2 / Redundancy: 7.3 % / Biso Wilson estimate: 20.49 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.258 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.094 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.683 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QYO

4qyo


Resolution: 2.2→32.05 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.63
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2115 4.83 %Random selection
Rwork0.2066 ---
obs0.2086 4359 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7061 0 0 365 7426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037234
X-RAY DIFFRACTIONf_angle_d0.6829825
X-RAY DIFFRACTIONf_dihedral_angle_d11.7322577
X-RAY DIFFRACTIONf_chiral_restr0.0261121
X-RAY DIFFRACTIONf_plane_restr0.0031256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25120.32371540.27592733X-RAY DIFFRACTION100
2.2512-2.30750.3351400.26362792X-RAY DIFFRACTION100
2.3075-2.36990.29741340.25512772X-RAY DIFFRACTION100
2.3699-2.43960.2911310.2642788X-RAY DIFFRACTION100
2.4396-2.51830.29791550.25662763X-RAY DIFFRACTION100
2.5183-2.60830.31721200.25442842X-RAY DIFFRACTION100
2.6083-2.71260.2681300.2422760X-RAY DIFFRACTION100
2.7126-2.8360.29441430.23022760X-RAY DIFFRACTION100
2.836-2.98540.28431400.22492798X-RAY DIFFRACTION100
2.9854-3.17230.29341550.22862778X-RAY DIFFRACTION100
3.1723-3.4170.25831210.21162757X-RAY DIFFRACTION100
3.417-3.76040.23431530.182788X-RAY DIFFRACTION100
3.7604-4.30340.18831460.16422786X-RAY DIFFRACTION100
4.3034-5.41760.15811480.14282739X-RAY DIFFRACTION100
5.4176-32.05380.19651450.16062785X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 0.0893 Å / Origin y: -18.6189 Å / Origin z: 34.3203 Å
111213212223313233
T0.1016 Å20.0042 Å2-0.0133 Å2-0.1394 Å20.0006 Å2--0.148 Å2
L0.0996 °2-0.0457 °20.0471 °2-0.2792 °20.1023 °2--0.7522 °2
S-0.0155 Å °0.0041 Å °0.0244 Å °-0.0685 Å °0.0053 Å °0.0405 Å °-0.0573 Å °0.0096 Å °0.0086 Å °
Refinement TLS groupSelection details: all

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