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- PDB-6w05: Crystal structure of Fab356 in complex with NPNA2 peptide from ci... -

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Basic information

Entry
Database: PDB / ID: 6w05
TitleCrystal structure of Fab356 in complex with NPNA2 peptide from circumsporozoite protein
Components
  • Fab356 heavy chain
  • Fab356 light chain
  • NPNA2 peptide
KeywordsIMMUNE SYSTEM / Malaria / Sporozoite / Circumsporozoite protein / Antibody
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
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: 2.516 Å
AuthorsPholcharee, T. / Oyen, D. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
Citation
Journal: Nat Commun / Year: 2021
Title: Structural and biophysical correlation of anti-NANP antibodies with in vivo protection against P. falciparum.
Authors: Pholcharee, T. / Oyen, D. / Flores-Garcia, Y. / Gonzalez-Paez, G. / Han, Z. / Williams, K.L. / Volkmuth, W. / Emerling, D. / Locke, E. / Richter King, C. / Zavala, F. / Wilson, I.A.
#1: Journal: Biorxiv / Year: 2020
Title: Structural and biophysical correlation of anti-NANP antibodies with in vivo protection against P. falciparum
Authors: Pholcharee, T. / Oyen, D. / Flores-Garcia, Y. / Gonzalez-Paez, G. / Han, Z. / Williams, K.L. / Volkmuth, W. / Emerling, D. / Locke, E. / King, C.R. / Zavala, F. / Wilson, I.A.
History
DepositionFeb 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Fab356 heavy chain
L: Fab356 light chain
P: NPNA2 peptide


Theoretical massNumber of molelcules
Total (without water)48,1163
Polymers48,1163
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-30 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.157, 81.728, 84.023
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 Fab356 heavy chain


Mass: 24242.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab356 light chain


Mass: 23062.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide NPNA2 peptide


Mass: 810.812 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 9.6 / Details: 40% PEG600, 0.1 M CHES, pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2018
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.516→50 Å / Num. obs: 15560 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.9 / Rpim(I) all: 0.058 / Rsym value: 0.144 / Net I/σ(I): 13.6
Reflection shellResolution: 2.52→2.56 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 773 / CC1/2: 0.547 / Rpim(I) all: 0.445 / Rsym value: 1.053

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model

Resolution: 2.516→43.262 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7
RfactorNum. reflection% reflection
Rfree0.256 748 4.82 %
Rwork0.2085 --
obs0.2109 15512 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.516→43.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 0 0 22 3359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043422
X-RAY DIFFRACTIONf_angle_d0.6514664
X-RAY DIFFRACTIONf_dihedral_angle_d12.3822010
X-RAY DIFFRACTIONf_chiral_restr0.044522
X-RAY DIFFRACTIONf_plane_restr0.004602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5164-2.71060.35241500.29582883X-RAY DIFFRACTION99
2.7106-2.98340.34161340.27352906X-RAY DIFFRACTION100
2.9834-3.41490.2661510.24282941X-RAY DIFFRACTION100
3.4149-4.30180.23991580.19332944X-RAY DIFFRACTION100
4.3018-43.2620.22351550.16933090X-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)
11.8977-0.8194-0.50691.7610.71811.6155-0.138-0.73390.59580.62740.9231-0.019-0.78030.8706-0.5930.80310.01590.05590.6622-0.30710.709326.56613.459815.5625
23.2875-0.2877-0.81032.1223-0.6312.64380.2868-0.66270.42790.50310.2887-0.2358-0.44580.2139-0.50210.57760.01770.14020.5406-0.12040.467618.699.855615.3971
32.6879-0.87890.00322.7449-0.29442.88120.2801-0.41160.6920.06080.446-0.0353-0.74940.3832-0.65840.65990.10520.24330.4648-0.11110.632420.960110.51858.6106
43.8322-0.5784-1.56242.1843-1.09062.0209-0.2379-0.34590.12190.14630.17-0.27690.06030.20220.10280.29130.0117-0.03120.3686-0.09130.350745.2579-11.8751-2.1127
54.0425-1.3877-0.16323.03690.20473.8692-0.0092-0.34690.41580.11280.1586-0.62110.1790.1007-0.15810.2791-0.022-0.04920.3343-0.03820.448254.539-12.1138-0.6506
63.25152.1292-3.13852.9263-2.33943.48070.64660.30040.6423-0.29680.15360.6598-0.2445-0.1543-0.63570.51420.0811-0.03110.53390.02290.468118.7633.2654-12.5725
71.02410.6179-0.86541.8879-0.21772.44040.1960.32290.3449-0.19570.2830.1497-0.5522-0.1886-0.42150.39740.09620.14430.42380.06980.502917.622212.5598-6.5999
80.4160.2282-0.52481.919-0.84082.51160.34510.10980.5151-0.33460.1720.0961-0.4717-0.3406-0.42380.4592-0.01080.05540.39980.09340.37620.18986.7954-10.8214
92.7752-0.79251.87223.5735-2.37577.41470.17020.2553-0.20620.407-0.0257-0.4227-0.01691.0887-0.04310.33810.031-0.02630.3527-0.08420.481844.4924-23.4665-3.3958
101.7853-0.62730.76482.2335-2.04392.6691-0.0978-0.07-0.17580.17860.36430.1935-0.3803-0.2868-0.27540.30410.00360.02430.3886-0.01220.34435.3097-12.9464-11.4644
111.1208-0.82540.42073.9708-1.42320.94970.24690.3095-0.23-0.8171-0.38150.28970.0164-0.23960.04850.31020.0182-0.01350.4011-0.08710.416729.0625-25.825-9.0547
121.5612-0.6603-0.50743.9665-1.7983.81420.16930.20350.2816-0.61220.11820.20250.13760.1186-0.25080.32780.00910.04250.3505-0.04510.349734.794-7.2463-9.7667
131.3569-0.09050.0591.9659-1.25261.1737-0.1379-0.092-0.3060.14830.22240.2528-0.0673-0.2943-0.07710.2770.0549-0.03580.3799-0.02730.377835.3585-26.768-4.4956
141.5341-0.172-0.37892.9342-1.95762.42090.15730.4653-0.1091-0.7027-0.2813-0.16060.376-0.1030.21360.42860.0937-0.01660.4152-0.10170.363135.2022-23.191-16.5567
155.86793.18082.1887.97194.80665.6180.7692-1.13510.9368-1.8309-0.9359-0.7159-1.5624-0.93120.00610.74570.17320.17770.7039-0.00640.66388.264716.680610.3744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 33 )
2X-RAY DIFFRACTION2chain 'H' and (resid 34 through 83 )
3X-RAY DIFFRACTION3chain 'H' and (resid 84 through 122 )
4X-RAY DIFFRACTION4chain 'H' and (resid 123 through 199 )
5X-RAY DIFFRACTION5chain 'H' and (resid 200 through 225 )
6X-RAY DIFFRACTION6chain 'L' and (resid 1 through 18 )
7X-RAY DIFFRACTION7chain 'L' and (resid 19 through 61 )
8X-RAY DIFFRACTION8chain 'L' and (resid 62 through 112 )
9X-RAY DIFFRACTION9chain 'L' and (resid 113 through 127 )
10X-RAY DIFFRACTION10chain 'L' and (resid 128 through 143 )
11X-RAY DIFFRACTION11chain 'L' and (resid 144 through 154 )
12X-RAY DIFFRACTION12chain 'L' and (resid 155 through 173 )
13X-RAY DIFFRACTION13chain 'L' and (resid 174 through 196 )
14X-RAY DIFFRACTION14chain 'L' and (resid 197 through 212 )
15X-RAY DIFFRACTION15chain 'P' and (resid 1 through 8 )

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