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- PDB-6wg2: Crystal structure of Fab239 in complex with NPNA4 peptide from ci... -

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Basic information

Entry
Database: PDB / ID: 6wg2
TitleCrystal structure of Fab239 in complex with NPNA4 peptide from circumsporozoite protein
Components
  • Fab239 heavy chain
  • Fab239 light chain
  • NPNA4 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: 2.534 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
DepositionApr 4, 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: Fab239 heavy chain
I: Fab239 heavy chain
L: Fab239 light chain
M: Fab239 light chain
P: NPNA4 peptide


Theoretical massNumber of molelcules
Total (without water)97,2505
Polymers97,2505
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-57 kcal/mol
Surface area36850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.166, 55.706, 115.732
Angle α, β, γ (deg.)90.00, 98.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab239 heavy chain


Mass: 24197.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab239 light chain


Mass: 23614.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide NPNA4 peptide


Mass: 1627.654 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.: 106 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG6000, 0.1 M HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 13, 2019
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.534→50 Å / Num. obs: 31852 / % possible obs: 91.9 % / Redundancy: 3.7 % / CC1/2: 0.88 / Rpim(I) all: 0.082 / Rsym value: 0.145 / Net I/σ(I): 7.9
Reflection shellResolution: 2.534→2.58 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1613 / CC1/2: 0.521 / Rpim(I) all: 0.522 / Rsym value: 0.898 / % possible all: 93.6

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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: 2.534→32.805 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.19
RfactorNum. reflection% reflection
Rfree0.2464 1591 5 %
Rwork0.1945 --
obs0.1971 31821 91.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.534→32.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 0 106 6696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026753
X-RAY DIFFRACTIONf_angle_d0.5659220
X-RAY DIFFRACTIONf_dihedral_angle_d14.253968
X-RAY DIFFRACTIONf_chiral_restr0.0431046
X-RAY DIFFRACTIONf_plane_restr0.0051188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.534-2.61550.34421400.28162587X-RAY DIFFRACTION87
2.6155-2.70890.3671580.27452681X-RAY DIFFRACTION91
2.7089-2.81730.34871360.25412672X-RAY DIFFRACTION89
2.8173-2.94550.31141440.25822761X-RAY DIFFRACTION93
2.9455-3.10070.28191490.24042764X-RAY DIFFRACTION93
3.1007-3.29480.25761470.21532837X-RAY DIFFRACTION94
3.2948-3.54890.28621190.19642798X-RAY DIFFRACTION93
3.5489-3.90550.23211640.18282668X-RAY DIFFRACTION90
3.9055-4.46940.18871420.15832850X-RAY DIFFRACTION94
4.4694-5.62640.171450.14442747X-RAY DIFFRACTION90
5.6264-32.8050.22721470.16762865X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.74330.76360.6463.0723-0.10083.58820.4952-0.07760.1639-0.60170.11790.57510.1891-1.2302-0.48330.3640.0581-0.02120.5660.16820.35466.79815.02744.4016
22.301521.07932-6.55220.50611.7246-4.52011.75184.0916-2.3225-3.48280.54914.66160.59080.9150.0234-0.43051.2248-0.08420.5984-0.79742.740.5469
31.9772-1.3598-0.48622.821-0.37051.77250.07990.0496-0.2072-0.1848-0.11120.19410.3177-0.03920.04970.2874-0.0390.01590.2348-0.05740.20929.1672-13.6749.8774
41.8036-1.00190.662.28060.99692.4179-0.05640.17190.01490.18240.05520.01650.09910.1369-0.03380.3057-0.05030.05970.21770.02170.22531.4228-13.42129.6024
50.83960.10540.14591.28880.27511.41830.1957-0.1818-0.03860.20560.0604-0.09690.4675-0.0086-0.25740.7260.0564-0.07630.36260.0030.414651.2727-30.995534.1667
61.2590.0497-0.14282.8424-0.2623.514-0.00840.1964-0.0915-0.0660.12620.1832-0.2158-0.2499-0.06210.2020.02550.02480.28490.0040.23773.17711.100518.3547
70.2664-0.15460.06541.41661.79492.50670.0010.02390.08370.1406-0.11360.06510.1286-0.1510.12070.2805-0.00380.01490.24770.05430.2732.255814.371341.1932
81.4579-0.2013-0.94451.2893-1.2474.2921-0.0459-0.12050.03710.0686-0.0852-0.28390.04410.17320.07850.2972-0.0784-0.03570.2996-0.02150.28746.25742.014925.1021
91.5622-0.29191.13881.10240.07774.2611-0.051-0.0514-0.0020.2310.0599-0.0937-0.42560.15840.00110.3618-0.0056-0.00530.186-0.00130.254137.62912.69720.9372
101.2034-0.65280.25021.8214-0.28320.65610.0853-0.1747-0.32850.16690.2713-0.4708-0.00090.019-0.34880.3824-0.0046-0.12290.3887-0.0680.446858.9615-20.574535.4405
113.046-2.8266-1.8653.26621.08481.76280.0025-0.00640.052-0.05090.0118-0.037-0.07090.29570.0160.33410.0423-0.07950.4369-0.05290.286961.7611-16.829732.6033
125.1455-2.0428-2.07871.99660.81511.40640.18070.21170.22550.1249-0.189-0.1987-0.11680.1750.13630.52090.0267-0.10960.3587-0.01040.323857.9447-15.696431.1617
132.1699-1.8071-0.34162.77350.52871.85180.18130.01730.1027-0.2419-0.3068-0.02390.04580.06380.10880.48070.02580.08630.4702-0.00560.350769.4004-21.913331.6637
141.8175-0.4797-0.44291.97761.44781.50890.09640.12720.2155-0.04230.0172-0.2928-0.32930.0362-0.11390.38910.05220.0550.33510.08130.300910.968124.06714.4019
150.53270.24510.77810.74630.62371.2160.1230.13660.21260.07850.0342-0.3032-0.25730.0036-0.13630.35360.04710.07090.2770.09120.299210.931424.0721.1959
161.6137-0.37311.00981.6449-0.91212.96420.06610.04090.04870.0237-0.0227-0.16270.01710.27-0.00780.33030.01760.00760.2812-0.03150.302617.085924.531651.2418
178.554-0.0004-0.7142.3145-0.16192.25450.28450.1423-0.30660.36850.1202-0.19290.0002-0.2335-0.44340.3122-0.00010.03270.1276-0.02860.244130.22711.03663.1282
182.3396-2.1658-1.73072.10751.84781.8725-0.02850.2979-0.3030.1305-0.41390.1734-0.2766-0.1420.34930.21940.02870.13940.19670.05570.434118.46910.73856.2209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'P' and (resid 12 through 16 )
2X-RAY DIFFRACTION2chain 'P' and (resid 17 through 17 )
3X-RAY DIFFRACTION3chain 'H' and (resid 1 through 60 )
4X-RAY DIFFRACTION4chain 'H' and (resid 61 through 119 )
5X-RAY DIFFRACTION5chain 'H' and (resid 120 through 215 )
6X-RAY DIFFRACTION6chain 'I' and (resid 2 through 76 )
7X-RAY DIFFRACTION7chain 'I' and (resid 77 through 215 )
8X-RAY DIFFRACTION8chain 'L' and (resid 1 through 18 )
9X-RAY DIFFRACTION9chain 'L' and (resid 19 through 103 )
10X-RAY DIFFRACTION10chain 'L' and (resid 104 through 129 )
11X-RAY DIFFRACTION11chain 'L' and (resid 130 through 151 )
12X-RAY DIFFRACTION12chain 'L' and (resid 152 through 175 )
13X-RAY DIFFRACTION13chain 'L' and (resid 176 through 213 )
14X-RAY DIFFRACTION14chain 'M' and (resid 1 through 75 )
15X-RAY DIFFRACTION15chain 'M' and (resid 76 through 114 )
16X-RAY DIFFRACTION16chain 'M' and (resid 115 through 213 )
17X-RAY DIFFRACTION17chain 'P' and (resid 2 through 6 )
18X-RAY DIFFRACTION18chain 'P' and (resid 7 through 11 )

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