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- PDB-6phg: Predicted germline variant of human transmission blocking antibod... -

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Basic information

Entry
Database: PDB / ID: 6phg
TitlePredicted germline variant of human transmission blocking antibody 2544
Components
  • Germline 2544 Antibody Fab, Heavy Chain
  • Germline 2544 Antibody Fab, Light Chain
KeywordsIMMUNE SYSTEM / Fab / Complex / Antigen / Immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMcLeod, B.R. / Julien, J.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1108403 Canada
CitationJournal: Nat Commun / Year: 2019
Title: Potent antibody lineage against malaria transmission elicited by human vaccination with Pfs25.
Authors: McLeod, B. / Miura, K. / Scally, S.W. / Bosch, A. / Nguyen, N. / Shin, H. / Kim, D. / Volkmuth, W. / Ramisch, S. / Chichester, J.A. / Streatfield, S. / Woods, C. / Schief, W.R. / Emerling, D. ...Authors: McLeod, B. / Miura, K. / Scally, S.W. / Bosch, A. / Nguyen, N. / Shin, H. / Kim, D. / Volkmuth, W. / Ramisch, S. / Chichester, J.A. / Streatfield, S. / Woods, C. / Schief, W.R. / Emerling, D. / King, C.R. / Julien, J.P.
History
DepositionJun 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 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: Germline 2544 Antibody Fab, Heavy Chain
B: Germline 2544 Antibody Fab, Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4203
Polymers48,3282
Non-polymers921
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-26 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.843, 60.557, 61.079
Angle α, β, γ (deg.)90.00, 113.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-379-

HOH

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Components

#1: Antibody Germline 2544 Antibody Fab, Heavy Chain


Mass: 24482.178 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 Germline 2544 Antibody Fab, Light Chain


Mass: 23845.537 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M sodium acetate pH 4.5, 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 29727 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.034 / Net I/σ(I): 13.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4002 / CC1/2: 0.776 / Rpim(I) all: 0.247 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house model

Resolution: 2→35.782 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.32
RfactorNum. reflection% reflection
Rfree0.2278 1999 6.73 %
Rwork0.1817 --
obs0.1848 29699 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→35.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3231 0 6 197 3434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043316
X-RAY DIFFRACTIONf_angle_d0.6964516
X-RAY DIFFRACTIONf_dihedral_angle_d10.1261967
X-RAY DIFFRACTIONf_chiral_restr0.046503
X-RAY DIFFRACTIONf_plane_restr0.004578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.37521290.29051958X-RAY DIFFRACTION100
2.05-2.10540.32921500.25691987X-RAY DIFFRACTION100
2.1054-2.16740.27811370.23941953X-RAY DIFFRACTION100
2.1674-2.23730.2531440.2181961X-RAY DIFFRACTION100
2.2373-2.31730.26531420.21691966X-RAY DIFFRACTION100
2.3173-2.410.27991330.20681966X-RAY DIFFRACTION100
2.41-2.51970.28251450.2051977X-RAY DIFFRACTION100
2.5197-2.65250.23881420.20461974X-RAY DIFFRACTION100
2.6525-2.81860.24761530.20411956X-RAY DIFFRACTION100
2.8186-3.03610.22071500.1981985X-RAY DIFFRACTION100
3.0361-3.34150.21721390.19011983X-RAY DIFFRACTION100
3.3415-3.82450.24161520.16891987X-RAY DIFFRACTION100
3.8245-4.81660.18411400.13521997X-RAY DIFFRACTION100
4.8166-35.78750.19011430.15992050X-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)
14.3829-0.9449-0.88942.21050.70263.795-0.2045-0.36060.15010.14270.10390.0019-0.23990.08380.08530.2230.0554-0.03680.2674-0.02610.182526.298634.120272.9122
23.8317-1.9262-3.77131.90222.33594.4194-0.12780.1752-0.0261-0.13480.0553-0.0693-0.19810.02910.05550.29820.0073-0.03350.3961-0.02970.238929.14428.160960.0354
33.9114-0.5272-1.83212.56340.19361.865-0.3592-0.5255-0.00940.36550.47490.3939-0.0449-0.2174-0.14740.42570.2067-0.00090.52110.11550.3179-0.443535.803677.0701
43.4389-0.22670.00733.01110.94493.1575-0.2272-0.6809-0.84190.49490.15550.35050.76520.09620.04350.46470.17120.08030.41080.14960.5193-5.564630.290174.7815
54.10340.97270.1925.50922.0137.2591-0.20080.85740.4311-0.2762-0.12230.3642-0.6726-0.28030.29490.42130.1724-0.05590.58760.06880.333610.584239.372348.7369
68.1891-1.271-0.96598.1493-0.00845.2925-0.0980.97011.4936-0.6092-0.1166-0.491-0.76140.27710.25150.4246-0.0272-0.070.41270.07630.466223.966335.125651.005
76.6188-2.552-0.1832.79080.44772.9299-0.02190.69-0.3975-0.1491-0.28210.3608-0.1079-0.63230.26330.2620.0716-0.02060.4427-0.04970.291316.858828.821450.0118
86.38430.1188-0.29995.12821.21815.0023-0.22660.09641.1240.0191-0.0543-0.1896-0.4698-0.17510.12550.3550.03740.01290.25510.04590.292618.952838.288255.0492
93.2229-0.7219-0.03771.77280.42872.6918-0.1508-0.3749-0.40260.28230.18380.15730.51920.2249-0.05180.26270.06970.02980.29590.04170.3503-12.298139.18365.0671
102.78070.00250.10591.12820.12.7195-0.1941-0.2868-0.15490.16540.24030.05020.1850.2137-0.00850.26950.07130.02280.29310.06430.272-10.678143.073267.6427
114.3386-1.7162-3.39712.65482.1477.0303-0.08150.3096-0.4621-0.0033-0.04440.0782-0.2312-0.86220.10050.25330.03290.00540.34190.04250.3714-20.915342.410163.6522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 115 )
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 146 )
4X-RAY DIFFRACTION4chain 'A' and (resid 147 through 227 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 22 )
6X-RAY DIFFRACTION6chain 'B' and (resid 23 through 42 )
7X-RAY DIFFRACTION7chain 'B' and (resid 43 through 95 )
8X-RAY DIFFRACTION8chain 'B' and (resid 96 through 109 )
9X-RAY DIFFRACTION9chain 'B' and (resid 110 through 153 )
10X-RAY DIFFRACTION10chain 'B' and (resid 154 through 191 )
11X-RAY DIFFRACTION11chain 'B' and (resid 192 through 216 )

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