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- PDB-6e64: Crystal structure of malaria transmission-blocking antibody 85RF45.1 -

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Basic information

Entry
Database: PDB / ID: 6.0E+64
TitleCrystal structure of malaria transmission-blocking antibody 85RF45.1
Components
  • 85RF45.1 Fab heavy chain
  • 85RF45.1 Fab light chain
KeywordsIMMUNE SYSTEM / malaria / transmission-blocking / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.15 Å
AuthorsKundu, P. / Semesi, A. / Julien, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1108403 United States
CitationJournal: Nat Commun / Year: 2018
Title: Structural delineation of potent transmission-blocking epitope I on malaria antigen Pfs48/45.
Authors: Kundu, P. / Semesi, A. / Jore, M.M. / Morin, M.J. / Price, V.L. / Liang, A. / Li, J. / Miura, K. / Sauerwein, R.W. / King, C.R. / Julien, J.P.
History
DepositionJul 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
H: 85RF45.1 Fab heavy chain
L: 85RF45.1 Fab light chain
A: 85RF45.1 Fab heavy chain
B: 85RF45.1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)94,6014
Polymers94,6014
Non-polymers00
Water00
1
H: 85RF45.1 Fab heavy chain
L: 85RF45.1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,3012
Polymers47,3012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-23 kcal/mol
Surface area19500 Å2
MethodPISA
2
A: 85RF45.1 Fab heavy chain
B: 85RF45.1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,3012
Polymers47,3012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-24 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.879, 86.522, 139.872
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 85RF45.1 Fab heavy chain


Mass: 23942.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Homo sapiens (human)
#2: Antibody 85RF45.1 Fab light chain


Mass: 23357.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Homo sapiens (human)
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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium thiocyanate, pH 6.9, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.15→43.4 Å / Num. obs: 15740 / % possible obs: 99.8 % / Redundancy: 12.9 % / Net I/σ(I): 7.2
Reflection shellResolution: 3.15→3.25 Å / Redundancy: 11.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1394 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 3.15→43.372 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.64
RfactorNum. reflection% reflection
Rfree0.2792 781 4.99 %
Rwork0.246 --
obs0.2477 15637 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.15→43.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6542 0 0 0 6542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046708
X-RAY DIFFRACTIONf_angle_d0.7869140
X-RAY DIFFRACTIONf_dihedral_angle_d20.3052418
X-RAY DIFFRACTIONf_chiral_restr0.0481028
X-RAY DIFFRACTIONf_plane_restr0.0051164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1463-3.34340.39621280.35362409X-RAY DIFFRACTION99
3.3434-3.60140.34271280.31342444X-RAY DIFFRACTION100
3.6014-3.96360.32781280.27182447X-RAY DIFFRACTION100
3.9636-4.53660.25661280.2332454X-RAY DIFFRACTION99
4.5366-5.71360.22371320.19772489X-RAY DIFFRACTION100
5.7136-43.37640.24661370.21052613X-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)
1-0.0284-0.0866-0.06080.0043-0.01320.0157-0.1902-0.176-0.08410.0790.0826-0.3855-0.4426-0.3136-00.4180.0569-0.10020.5465-0.05230.4082-49.9047-1.87139.9925
2-0.18680.19130.14330.0411-0.1645-0.0028-0.127-0.1313-0.001-0.2794-0.1144-0.0729-0.02540.106600.6397-0.04820.04260.39010.01640.2964-58.23719.132-20.5297
30.07110.0260.04460.0201-0.05240.04990.0249-0.0479-0.1765-0.2191-0.40350.22380.0478-0.090200.5754-0.01050.16160.3741-0.04150.3263-64.659512.2874-30.4177
4-0.02430.00230.03190.1444-0.08250.0889-0.06-0.144-0.4419-0.08630.2464-0.5556-0.1012-0.15-00.23220.0397-0.04490.3543-0.03210.4433-49.5846-18.5209-1.3792
50.00780.0063-0.0060.0152-0.0252-0.0021-0.14710.0914-0.2240.1391-0.0136-0.2358-0.048-0.0625-00.292-0.00090.10670.4193-0.08070.5251-59.0685-24.22655.7722
60.0095-0.00290.02770.00640.0205-0.0176-0.2602-0.2791-0.083-0.1077-0.21150.00090.1329-0.0225-00.46490.0231-0.03830.6676-0.00750.6206-47.6846-27.22470.1945
7-0.3142-0.18820.26830.04990.0725-0.0752-0.5106-0.50110.0132-0.7011-0.0412-0.08580.1867-0.0771-00.2493-0.0299-0.10880.4197-0.00310.3415-53.1753-16.3527-6.2771
80.09450.0240.02170.01690.02110.06750.31290.50530.04010.1554-0.09790.03360.20570.167400.6051-0.0588-0.10690.41460.10620.472-50.08163.4913-29.6837
90.00170.008-0.03210.0510.0767-0.0111-0.0051-0.0765-0.3433-0.12350.02980.5010.00020.6487-00.7-0.1196-0.04270.41870.11870.6521-49.6695-2.1428-23.9934
100.0532-0.052-0.0574-0.00310.0369-0.0041-0.1530.3519-0.25980.04220.4482-0.29220.0203-0.022100.46580.06750.09920.5462-0.11040.4563-44.7642.0775-32.1424
11-0.1153-0.11770.05840.0773-0.01950.04850.19490.0564-0.15810.1473-0.14520.03650.03030.078800.59350.02330.12890.46060.06360.4548-53.7869-43.5779-60.1284
12-0.0257-0.02140.0590.12010.00250.0622-0.06560.02230.0088-0.0514-0.0330.11460.06670.1798-00.50170.0270.15370.44830.06540.3144-52.0754-45.3775-56.7486
13-0.23110.05540.0390.152-0.05940.1085-0.0349-0.03370.04-0.3244-0.06040.0154-0.1319-0.0225-00.3927-0.06870.12860.37580.0280.4847-61.5705-52.971-22.2165
14-0.61640.1794-0.1762-0.01230.04610.031-1.03880.43210.22921.79380.11-0.2317-0.0823-0.06850-1.0696-0.0046-0.17620.27320.060.4569-52.5972-24.0623-48.3772
150.0470.10340.31650.19110.0756-0.1414-0.0241-0.10780.174-0.0368-0.00680.02230.21850.1696-00.45690.0307-0.00680.36510.01780.5607-47.8243-44.541-20.8064
160.0043-0.07530.02650.04960.03930.1037-0.2213-0.36070.3009-0.04220.33790.2956-0.3445-0.0749-00.62820.1541-0.01340.56930.02540.3811-57.71171.681111.4469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 103 )
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 177 )
3X-RAY DIFFRACTION3chain 'A' and (resid 178 through 214 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 48 )
5X-RAY DIFFRACTION5chain 'B' and (resid 49 through 61 )
6X-RAY DIFFRACTION6chain 'B' and (resid 62 through 75 )
7X-RAY DIFFRACTION7chain 'B' and (resid 76 through 113 )
8X-RAY DIFFRACTION8chain 'B' and (resid 114 through 150 )
9X-RAY DIFFRACTION9chain 'B' and (resid 151 through 171 )
10X-RAY DIFFRACTION10chain 'B' and (resid 172 through 209 )
11X-RAY DIFFRACTION11chain 'H' and (resid 1 through 59 )
12X-RAY DIFFRACTION12chain 'H' and (resid 60 through 119 )
13X-RAY DIFFRACTION13chain 'H' and (resid 120 through 214 )
14X-RAY DIFFRACTION14chain 'L' and (resid 1 through 113 )
15X-RAY DIFFRACTION15chain 'L' and (resid 114 through 209 )
16X-RAY DIFFRACTION16chain 'A' and (resid 1 through 33 )

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