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- PDB-6e65: Crystal structure of malaria transmission-blocking antibody TB31F -

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Basic information

Entry
Database: PDB / ID: 6.0E+65
TitleCrystal structure of malaria transmission-blocking antibody TB31F
Components
  • TB31F Fab heavy chain
  • TB31F Fab light chain
KeywordsIMMUNE SYSTEM / malaria / transmission-blocking / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 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 1.2Nov 6, 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
L: TB31F Fab light chain
H: TB31F Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,0112
Polymers47,0112
Non-polymers00
Water9,548530
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-24 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.680, 70.720, 115.360
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 TB31F Fab light chain


Mass: 23169.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody TB31F Fab heavy chain


Mass: 23841.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, pH 7.5, 10% (v/v) 2-propanol, 20% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.999977 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999977 Å / Relative weight: 1
ReflectionResolution: 1.5→44.7 Å / Num. obs: 73693 / % possible obs: 100 % / Redundancy: 13 % / Net I/σ(I): 15.9
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 12770 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.5→44.698 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.28
RfactorNum. reflection% reflection
Rfree0.187 2000 2.72 %
Rwork0.1749 --
obs0.1752 73616 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→44.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 0 530 3812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063367
X-RAY DIFFRACTIONf_angle_d0.8994591
X-RAY DIFFRACTIONf_dihedral_angle_d19.8491213
X-RAY DIFFRACTIONf_chiral_restr0.059515
X-RAY DIFFRACTIONf_plane_restr0.006586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.3161410.26775050X-RAY DIFFRACTION100
1.5375-1.57910.24481410.2465031X-RAY DIFFRACTION100
1.5791-1.62560.25521400.23315034X-RAY DIFFRACTION100
1.6256-1.6780.23891410.22385046X-RAY DIFFRACTION100
1.678-1.7380.24291420.21655108X-RAY DIFFRACTION100
1.738-1.80760.23891430.19765079X-RAY DIFFRACTION100
1.8076-1.88990.19861410.18565044X-RAY DIFFRACTION100
1.8899-1.98950.18441420.17125108X-RAY DIFFRACTION100
1.9895-2.11410.17571420.17215073X-RAY DIFFRACTION100
2.1141-2.27740.18971430.17035120X-RAY DIFFRACTION100
2.2774-2.50650.22251440.1825158X-RAY DIFFRACTION100
2.5065-2.86920.2111430.18245136X-RAY DIFFRACTION100
2.8692-3.61460.16361450.1625203X-RAY DIFFRACTION100
3.6146-44.7180.14761520.15155426X-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)
10.01970.008-0.03370.01090.01930.0262-0.1076-0.0289-0.0070.07760.03350.13990.2903-0.076500.1648-0.0045-0.00440.1315-0.02670.1911-1.8968-4.96891.4674
20.029-0.0342-0.02440.0271-0.01270.02410.04990.02080.086-0.212-0.137-0.04160.07770.095400.1220.0077-0.0420.1089-0.06350.0943-1.05540.8694-7.0437
30.0054-0.01410.01080.01420.00030.00880.080.0398-0.1784-0.2166-0.07330.10460.1827-0.0368-00.26960.13360.0641-0.2201-0.4453-0.21412.592-7.1555-10.9942
40.0234-0.032-0.07340.04490.04230.0879-0.06460.0831-0.0394-0.09250.03170.02640.06870.061900.13240.0066-0.01810.1134-0.02940.09640.7645-0.624-2.4568
5-0.01-0.0113-0.03250.0042-0.03570.0364-0.0252-0.00240.04380.0892-0.0349-0.06010.02670.000300.08310.0116-0.00450.06340.00140.1061-2.605310.914227.8245
60.00920.00860.00010.01570.01860.0285-0.03580.09250.0131-0.0394-0.00420.02480.0869-0.006300.09750.0081-0.00340.09130.01080.1144-7.0525.177319.4214
70.00390.0018-0.00160.00080.0004-0.0024-0.0826-0.0321-0.0338-0.1313-0.0988-0.1357-0.0580.044100.07420.0080.04390.12970.03630.18179.36246.286617.1993
80.00540.00590.01580.00690.00520.0167-0.00540.0044-0.0518-0.0574-0.00560.0637-0.0744-0.044100.08280.00520.00020.10060.01090.1154-12.78814.654927.5714
90.0048-0.0030.0055-0.00890.00490.00380.0769-0.0257-0.0422-0.05640.02640.04260.0442-0.0341-00.0764-0.00530.00530.06450.01230.1304-10.67283.694426.0121
100.0230.0090.01680.0083-0.00250.00920.0109-0.107-0.0901-0.02330.16260.02310.0616-0.158600.16810.00030.00690.05250.00070.1303-7.64351.767428.6627
110.1559-0.00210.02650.1056-0.12260.125-0.01950.23090.23780.4661-0.0194-0.21560.2761-0.1006-0-0.033-0.00060.03510.1820.01620.0677-2.55518.0385-10.8079
120.0298-0.01720.02490.23920.0890.10520.03380.059-0.0610.00870.055-0.02180.01470.0318-00.10750.0025-0.03510.06740.01360.10534.447219.408629.4563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'L' and (resid 26 through 48 )
3X-RAY DIFFRACTION3chain 'L' and (resid 49 through 68 )
4X-RAY DIFFRACTION4chain 'L' and (resid 69 through 106A)
5X-RAY DIFFRACTION5chain 'L' and (resid 107 through 137 )
6X-RAY DIFFRACTION6chain 'L' and (resid 138 through 161 )
7X-RAY DIFFRACTION7chain 'L' and (resid 162 through 173 )
8X-RAY DIFFRACTION8chain 'L' and (resid 174 through 187 )
9X-RAY DIFFRACTION9chain 'L' and (resid 188 through 197 )
10X-RAY DIFFRACTION10chain 'L' and (resid 198 through 210 )
11X-RAY DIFFRACTION11chain 'H' and (resid 1 through 111 )
12X-RAY DIFFRACTION12chain 'H' and (resid 112 through 214 )

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