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- PDB-4r3s: Crystal Structure of anti-MSP2 Fv fragment (mAb6D8)in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4r3s
TitleCrystal Structure of anti-MSP2 Fv fragment (mAb6D8)in complex with MSP2 11-23
Components
  • FV FRAGMENT(MAB6D8) HEAVY CHAIN
  • FV FRAGMENT(MAB6D8) LIGHT CHAIN
  • Merozoite surface protein
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 (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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.V. / MacRaild, C.A. / Seow, J. / Krishnarjuna, B. / Drinkwater, N. / Rouet, R. / Anders, R.F. / Christ, D. / McGowan, S. / Norton, R.S.
History
DepositionAug 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / reflns_shell ...pdbx_unobs_or_zero_occ_atoms / reflns_shell / struct_conn / struct_ref_seq_dif
Item: _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 protein


Theoretical massNumber of molelcules
Total (without water)26,0613
Polymers26,0613
Non-polymers00
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-14 kcal/mol
Surface area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.210, 64.340, 89.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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) / Strain (production host): BL21 (DE3)
#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) / Strain (production host): BL21 (DE3)
#3: Protein/peptide Merozoite surface protein


Mass: 1611.849 Da / Num. of mol.: 1 / Fragment: 11-23 / Source method: obtained synthetically
Details: This sequence occurs naturally in Plasmodium Falciparum
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q9GQZ3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsIN THIS PROTEIN, THE SEQUENCES OF THE ENTITY1 AND ENTITY2 WERE NOT AVAILABLE AT THE UNIPROT ...IN THIS PROTEIN, THE SEQUENCES OF THE ENTITY1 AND ENTITY2 WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 1.95 Å3/Da / Density % sol: 37.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 30% PEG 8000, 0.2M NACL, 0.1M NAOAC, pH 4.0, 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: May 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→52.315 Å / Num. all: 23184 / Num. obs: 23184 / % possible obs: 100 % / Observed criterion σ(F): 1.35 / Redundancy: 33.8 % / Rmerge(I) obs: 0.8825
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 32.4 % / Rmerge(I) obs: 2.01 / Mean I/σ(I) obs: 5.15 / Num. unique all: 2279 / % possible all: 100

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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: 1.7→52.315 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 17.57 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2004 1218 5.25 %RANDOM
Rwork0.1518 ---
obs0.1543 23184 99.99 %-
all-23184 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→52.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 0 370 2177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171898
X-RAY DIFFRACTIONf_angle_d1.6072595
X-RAY DIFFRACTIONf_dihedral_angle_d12.964690
X-RAY DIFFRACTIONf_chiral_restr0.089290
X-RAY DIFFRACTIONf_plane_restr0.008339
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.7-1.76810.26911310.20142396
1.7681-1.84860.24411400.16972394
1.8486-1.9460.22751350.1642387
1.946-2.0680.20021380.13912407
2.068-2.22760.19461220.13992428
2.2276-2.45180.1981400.15312425
2.4518-2.80660.20771270.16142449
2.8066-3.53590.16771300.14322492
3.5359-52.34010.18241550.13892588
Refinement TLS params.Method: refined / Origin x: -4.4092 Å / Origin y: -1.4233 Å / Origin z: 13.1768 Å
111213212223313233
T0.0275 Å2-0.0089 Å20.0042 Å2-0.0149 Å2-0.0011 Å2--0.0405 Å2
L0.5474 °2-0.1128 °2-0.0178 °2-0.3751 °20.0058 °2--0.9871 °2
S-0.0031 Å °-0.0073 Å °0.0091 Å °-0.0188 Å °-0.0273 Å °-0.0059 Å °-0.019 Å °-0.0119 Å °0.0125 Å °
Refinement TLS groupSelection details: all

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