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- PDB-5bk0: Crystal structure of 663 Fab bound to circumsporozoite protein NA... -

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Basic information

Entry
Database: PDB / ID: 5bk0
TitleCrystal structure of 663 Fab bound to circumsporozoite protein NANP 5-mer
Components
  • 663 Antibody, heavy chain
  • 663 Antibody, light chain
  • Circumsporozoite protein NANP 5-mer
KeywordsIMMUNE SYSTEM / Malaria / Circumsporozoite protein / Fab
Function / homology
Function and homology information


entry into host cell by a symbiont-containing vacuole / side of membrane / cell surface / plasma membrane / cytoplasm
Similarity search - Function
Plasmodium circumsporozoite protein / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsScally, S.W. / Bosch, A. / Triller, G. / Wardemann, H. / Julien, J.P.
CitationJournal: Immunity / Year: 2017
Title: Natural Parasite Exposure Induces Protective Human Anti-Malarial Antibodies.
Authors: Triller, G. / Scally, S.W. / Costa, G. / Pissarev, M. / Kreschel, C. / Bosch, A. / Marois, E. / Sack, B.K. / Murugan, R. / Salman, A.M. / Janse, C.J. / Khan, S.M. / Kappe, S.H.I. / Adegnika, ...Authors: Triller, G. / Scally, S.W. / Costa, G. / Pissarev, M. / Kreschel, C. / Bosch, A. / Marois, E. / Sack, B.K. / Murugan, R. / Salman, A.M. / Janse, C.J. / Khan, S.M. / Kappe, S.H.I. / Adegnika, A.A. / Mordmuller, B. / Levashina, E.A. / Julien, J.P. / Wardemann, H.
History
DepositionSep 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 26, 2020Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.3Apr 3, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 663 Antibody, light chain
B: 663 Antibody, heavy chain
C: 663 Antibody, light chain
D: 663 Antibody, heavy chain
E: Circumsporozoite protein NANP 5-mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5317
Polymers97,3475
Non-polymers1842
Water0
1
A: 663 Antibody, light chain
B: 663 Antibody, heavy chain
E: Circumsporozoite protein NANP 5-mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7654
Polymers49,6733
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-30 kcal/mol
Surface area19880 Å2
MethodPISA
2
C: 663 Antibody, light chain
D: 663 Antibody, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7653
Polymers47,6732
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-26 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.815, 132.674, 51.020
Angle α, β, γ (deg.)90.00, 93.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody 663 Antibody, light chain


Mass: 23881.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 663 Antibody, heavy chain


Mass: 23791.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide Circumsporozoite protein NANP 5-mer


Mass: 2000.006 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893*PLUS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM tri-sodium citrate pH 5.5, 20% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.15→40 Å / Num. obs: 20694 / % possible obs: 99.8 % / Redundancy: 3.9 % / Rpim(I) all: 0.102 / Net I/σ(I): 7.07
Reflection shellResolution: 3.15→3.25 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1829 / Rpim(I) all: 0.347 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SHELXPREPdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 663 Fab

Resolution: 3.15→38.297 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.12
RfactorNum. reflection% reflection
Rfree0.2735 1026 4.96 %
Rwork0.2345 --
obs0.2365 20687 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.15→38.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6536 0 12 0 6548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046706
X-RAY DIFFRACTIONf_angle_d0.9259159
X-RAY DIFFRACTIONf_dihedral_angle_d15.0333964
X-RAY DIFFRACTIONf_chiral_restr0.0551053
X-RAY DIFFRACTIONf_plane_restr0.0061178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.3160.34351440.31162782X-RAY DIFFRACTION100
3.316-3.52360.35181440.29212802X-RAY DIFFRACTION100
3.5236-3.79550.31761470.27612795X-RAY DIFFRACTION100
3.7955-4.1770.2751490.24072811X-RAY DIFFRACTION100
4.177-4.78050.21681410.19942802X-RAY DIFFRACTION100
4.7805-6.01910.25971460.2062816X-RAY DIFFRACTION100
6.0191-38.29980.24931550.20882853X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.15750.90220.21652.7714-0.29933.2894-0.21180.2246-0.8443-0.15740.49210.05160.0623-0.35180.22990.2927-0.0640.00420.3367-0.09520.535218.271338.2244-46.8476
23.24722.00541.91153.7972-0.08132.5306-0.11580.4738-1.2919-0.0573-0.3387-0.7280.86510.2536-0.50690.6805-0.06150.24280.4278-0.25010.527251.954344.9165-54.826
33.81282.84640.11912.666-0.41191.1805-0.0372-0.85260.52190.2344-0.24180.5883-0.9517-0.57720.03880.61370.21730.06290.5505-0.1190.408218.863554.51-31.763
42.58130.06740.21331.9521-0.65271.417-0.19280.46070.0472-0.3286-0.1675-0.20040.02210.12480.20360.4654-0.1291-0.01360.3521-0.05650.183545.906759.9394-54.704
52.1685-0.27332.14170.8598-0.93972.5651-0.1410.20230.32130.00760.26390.5491-0.5437-0.4683-0.16950.80320.25980.00810.9659-0.18161.040718.326100.4118-32.9243
66.47680.8396-0.32223.43111.18194.3249-0.0206-0.0490.6397-0.2181-0.1757-0.0738-0.91460.19740.09860.4276-0.0426-0.0670.25520.01010.278850.91393.8383-21.0996
73.8755-1.6440.18351.7179-1.15852.0577-0.52680.5167-0.19490.1591-0.07950.7424-0.4516-0.84450.59010.7279-0.0028-0.11420.7263-0.3010.859222.891682.9615-46.7581
82.470.4825-1.35661.9195-0.29313.55990.11170.01960.05660.1066-0.1692-0.0356-0.03050.06960.04080.3273-0.08550.00850.1871-0.03330.18744.950379.4968-20.1796
92.9714-1.71764.40164.2554-0.42567.8905-0.9090.0841-0.6914-0.20570.04732.12920.4444-0.4510.30890.4105-0.21110.06330.3409-0.00270.6056.480843.771-31.236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 213 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 106 )
4X-RAY DIFFRACTION4chain 'B' and (resid 107 through 214 )
5X-RAY DIFFRACTION5chain 'C' and (resid 3 through 113 )
6X-RAY DIFFRACTION6chain 'C' and (resid 114 through 213 )
7X-RAY DIFFRACTION7chain 'D' and (resid 2 through 119 )
8X-RAY DIFFRACTION8chain 'D' and (resid 120 through 214 )
9X-RAY DIFFRACTION9chain 'E' and (resid 2 through 8 )

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