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- PDB-6phh: Unliganded human transmission blocking antibody 2544 -

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Basic information

Entry
Database: PDB / ID: 6phh
TitleUnliganded human transmission blocking antibody 2544
Components
  • 2544 Antibody Fab, Heavy Chain
  • 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: 2.4 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
C: 2544 Antibody Fab, Heavy Chain
D: 2544 Antibody Fab, Light Chain
A: 2544 Antibody Fab, Heavy Chain
B: 2544 Antibody Fab, Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,14210
Polymers96,5904
Non-polymers5536
Water2,234124
1
C: 2544 Antibody Fab, Heavy Chain
D: 2544 Antibody Fab, Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6636
Polymers48,2952
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-31 kcal/mol
Surface area19460 Å2
MethodPISA
2
A: 2544 Antibody Fab, Heavy Chain
B: 2544 Antibody Fab, Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4794
Polymers48,2952
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-28 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.530, 43.650, 138.570
Angle α, β, γ (deg.)90.00, 111.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody 2544 Antibody Fab, Heavy Chain


Mass: 24460.242 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 2544 Antibody Fab, Light Chain


Mass: 23834.557 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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M sodium cacodylate HCl, pH 6.5, 1.0 M sodium citrate tribasic

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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: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 38316 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.055 / Net I/σ(I): 11.2
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4305 / CC1/2: 0.549 / Rpim(I) all: 0.298 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house model

Resolution: 2.4→38.976 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4
RfactorNum. reflection% reflection
Rfree0.2487 1915 5 %
Rwork0.2177 --
obs0.2192 38299 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→38.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6667 0 36 124 6827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026867
X-RAY DIFFRACTIONf_angle_d0.5519368
X-RAY DIFFRACTIONf_dihedral_angle_d11.5774056
X-RAY DIFFRACTIONf_chiral_restr0.0431048
X-RAY DIFFRACTIONf_plane_restr0.0041207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.38921330.35232522X-RAY DIFFRACTION100
2.46-2.52650.37591360.34342584X-RAY DIFFRACTION100
2.5265-2.60080.33431350.29512563X-RAY DIFFRACTION100
2.6008-2.68480.32761360.28542585X-RAY DIFFRACTION100
2.6848-2.78070.31711380.27332615X-RAY DIFFRACTION100
2.7807-2.8920.31911340.2722552X-RAY DIFFRACTION100
2.892-3.02360.32471350.27392577X-RAY DIFFRACTION100
3.0236-3.18290.23891370.25262585X-RAY DIFFRACTION100
3.1829-3.38220.25321370.23172605X-RAY DIFFRACTION100
3.3822-3.64320.23361360.21212593X-RAY DIFFRACTION100
3.6432-4.00950.23981380.20562612X-RAY DIFFRACTION100
4.0095-4.58890.21731360.17332591X-RAY DIFFRACTION100
4.5889-5.77850.19321400.17422654X-RAY DIFFRACTION100
5.7785-38.98140.22581440.18392746X-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)
11.5855-0.1410.66392.6108-0.11433.5375-0.0776-0.0382-0.09740.03870.08720.17270.0671-0.2007-0.00960.3560.00560.06830.20620.00480.447143.27128.366847.3996
24.5243-1.8053-0.27115.2029-1.79452.8458-0.11940.27920.8274-0.36930.31790.3587-0.7561-0.6795-0.10420.86070.1521-0.17490.47140.07240.56531.559730.734622.708
35.6188-0.9017-0.03673.1954-0.19853.5818-0.03790.0186-0.2213-0.06680.00960.43280.1008-0.62080.05390.2723-0.02790.09280.4401-0.01060.547722.00819.675652.469
43.3295-0.6683-1.00712.8099-0.32922.6728-0.22410.9689-0.0836-0.73450.35490.72270.1237-1.2354-0.19470.77280.0277-0.32161.07960.26630.80818.794122.488318.6705
51.3592-0.17580.12952.5821-0.80854.26120.00830.0574-0.04140.1466-0.0106-0.1641-0.02680.28960.02550.3596-0.02080.07480.21640.01030.380159.58831.293645.9176
63.1697-0.77380.17574.35051.77891.73530.22750.2473-0.44880.25270.1074-0.4091.03170.5683-0.22320.97250.1928-0.01420.4563-0.05940.450365.97638.573919.6212
74.6174-0.22-0.02643.69770.53374.97760.12560.2129-0.01080.365-0.0466-0.6957-0.10040.7699-0.06630.3513-0.0604-0.10.42520.05790.575481.231129.85846.9842
82.7080.14-0.30232.72411.65742.97930.05131.1856-0.0519-0.43180.5077-0.47650.10531.7086-0.50630.71630.13410.10221.1537-0.11830.490277.887916.526313.2117
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 126 )
2X-RAY DIFFRACTION2chain 'C' and (resid 127 through 228 )
3X-RAY DIFFRACTION3chain 'D' and (resid 1 through 112 )
4X-RAY DIFFRACTION4chain 'D' and (resid 113 through 217 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1 through 126 )
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 228 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 112 )
8X-RAY DIFFRACTION8chain 'B' and (resid 113 through 217 )

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