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- PDB-6azx: Crystal structure of the neutralizing anti-circumsporozoite prote... -

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Basic information

Entry
Database: PDB / ID: 6azx
TitleCrystal structure of the neutralizing anti-circumsporozoite protein 663 antibody
Components
  • 663 antibody, heavy chain
  • 663 antibody, light chain
KeywordsIMMUNE SYSTEM / Malaria / Circumsporozoite protein / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsScally, S.W. / Bosch, A. / Triller, G. / Wardemann, H. / Julien, J.P.
CitationJournal: Immunity / Year: 2017
Title: Natural Parasite Exposure Induces Protective Human Anti-Malarial Antibodies.
Authors: Triller, G. / Scally, S.W. / Costa, G. / Pissarev, M. / Kreschel, C. / Bosch, A. / Marois, E. / Sack, B.K. / Murugan, R. / Salman, A.M. / Janse, C.J. / Khan, S.M. / Kappe, S.H.I. / Adegnika, ...Authors: Triller, G. / Scally, S.W. / Costa, G. / Pissarev, M. / Kreschel, C. / Bosch, A. / Marois, E. / Sack, B.K. / Murugan, R. / Salman, A.M. / Janse, C.J. / Khan, S.M. / Kappe, S.H.I. / Adegnika, A.A. / Mordmuller, B. / Levashina, E.A. / Julien, J.P. / Wardemann, H.
History
DepositionSep 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 26, 2020Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.3Oct 4, 2023Group: 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 663 antibody, heavy chain
D: 663 antibody, light chain
A: 663 antibody, heavy chain
B: 663 antibody, light chain


Theoretical massNumber of molelcules
Total (without water)95,7594
Polymers95,7594
Non-polymers00
Water9,818545
1
A: 663 antibody, heavy chain
B: 663 antibody, light chain


Theoretical massNumber of molelcules
Total (without water)47,8802
Polymers47,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-25 kcal/mol
Surface area19070 Å2
MethodPISA
2
C: 663 antibody, heavy chain
D: 663 antibody, light chain


Theoretical massNumber of molelcules
Total (without water)47,8802
Polymers47,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-25 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.283, 138.085, 206.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-418-

HOH

21A-417-

HOH

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Components

#1: Antibody 663 antibody, heavy chain


Mass: 23894.855 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 663 antibody, light chain


Mass: 23984.752 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.99 Å3/Da / Density % sol: 58.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 200 mM di-ammonium hydrogen citrate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 67267 / % possible obs: 100 % / Redundancy: 5.7 % / Rpim(I) all: 0.058 / Net I/σ(I): 9.56
Reflection shellResolution: 2.1→2.2 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8643 / Rpim(I) all: 0.279 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
SHELXPREPdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A3I

5a3i


Resolution: 2.1→39.931 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 1999 2.97 %
Rwork0.206 --
obs0.207 67217 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→39.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6302 0 0 546 6848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026463
X-RAY DIFFRACTIONf_angle_d0.5848820
X-RAY DIFFRACTIONf_dihedral_angle_d12.8393829
X-RAY DIFFRACTIONf_chiral_restr0.0441007
X-RAY DIFFRACTIONf_plane_restr0.0051133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.3191460.28884580X-RAY DIFFRACTION100
2.1525-2.21070.23871410.26134618X-RAY DIFFRACTION100
2.2107-2.27580.31851390.24694613X-RAY DIFFRACTION100
2.2758-2.34920.30411400.24664633X-RAY DIFFRACTION100
2.3492-2.43320.24751440.24074607X-RAY DIFFRACTION100
2.4332-2.53060.28081380.23944600X-RAY DIFFRACTION100
2.5306-2.64570.25051440.23124640X-RAY DIFFRACTION100
2.6457-2.78520.25681380.22824624X-RAY DIFFRACTION100
2.7852-2.95960.26441430.22434686X-RAY DIFFRACTION100
2.9596-3.1880.24211420.21944637X-RAY DIFFRACTION100
3.188-3.50870.26691420.2064665X-RAY DIFFRACTION100
3.5087-4.0160.21221390.18914708X-RAY DIFFRACTION100
4.016-5.05810.20191500.15734716X-RAY DIFFRACTION100
5.0581-39.93830.19371530.18174891X-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)
13.3243-1.59030.17124.1733-0.84442.05070.0113-0.14850.11270.1382-0.0124-0.0047-0.11150.0536-0.00760.141-0.02530.01970.1358-0.01670.1671-5.027518.1131-0.2031
22.5137-0.42461.94493.07631.29355.0211-0.14660.7671-0.9452-0.64560.10430.64221.1258-0.46850.04120.6628-0.25120.04380.6262-0.21190.6171-24.899920.7946-24.3632
33.6726-0.18230.13772.9739-0.54114.51710.02710.6271-0.2673-0.48040.0065-0.23870.2260.2734-0.02830.22760.02490.06580.2366-0.05250.230410.78519.4613-15.5861
40.1341-0.05610.28920.0121-0.14680.4166-0.13521.2022-0.2043-0.4178-0.13810.14270.0864-0.36560.26960.67870.027-0.02241.3053-0.07840.3451-7.346325.1175-35.3295
57.1058-1.4466-1.62752.717-0.1983.4355-0.20581.10770.272-0.52270.10490.51590.0211-0.71830.08040.5708-0.0398-0.18431.08510.0440.4412-21.956731.926-32.87
61.65610.56950.162.16610.12673.59330.18191.99850.5731-1.0195-0.58660.1805-0.1855-0.50480.35610.65190.1029-0.12861.12220.18010.4332-20.005134.1921-35.2582
73.0891-1.7621-1.04285.84971.75662.54250.0333-0.0343-0.16710.2438-0.09920.03340.0724-0.070.08010.1409-0.0107-0.02190.14580.0310.14451.378952.4546-5.0342
83.17660.3121-1.14312.9618-2.83546.9911-0.16190.54970.7787-0.085-0.2345-0.2214-0.91671.4360.34110.4929-0.2151-0.13010.74240.19020.499620.461754.7712-26.7186
91.99250.8837-0.25442.8524-1.52264.04430.01950.44610.0197-0.31890.12260.2519-0.0989-0.3859-0.12030.24750.0807-0.03960.33760.0020.2266-13.407652.7019-20.3813
103.7537-0.09150.35353.1617-0.73644.5516-0.01230.49670.3949-0.40420.11630.2979-0.4514-0.492-0.09910.25110.0771-0.03420.26770.05680.2409-13.784656.368-20.4684
110.01890.0426-0.0330.292-0.06410.32310.08740.47050.1251-0.4516-0.478-0.16810.4411.49870.26730.50810.22010.18611.80450.38010.298914.610153.7169-39.675
124.756-1.1787-3.55844.97770.95834.31930.14210.8746-0.2134-0.4094-0.1143-0.31780.48931.0399-0.05350.58530.1899-0.0561.0149-0.1050.30849.924250.1578-40.9711
130.06940.0485-0.02780.08670.0780.01530.10220.6648-0.3469-1.0173-0.3485-0.22021.11761.70170.18320.66080.86680.50292.535-0.1623-0.121118.940148.3854-47.529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 119 )
2X-RAY DIFFRACTION2chain 'C' and (resid 120 through 213 )
3X-RAY DIFFRACTION3chain 'D' and (resid 1 through 101 )
4X-RAY DIFFRACTION4chain 'D' and (resid 102 through 118 )
5X-RAY DIFFRACTION5chain 'D' and (resid 119 through 150 )
6X-RAY DIFFRACTION6chain 'D' and (resid 151 through 211 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1 through 106 )
8X-RAY DIFFRACTION8chain 'A' and (resid 107 through 210 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 48 )
10X-RAY DIFFRACTION10chain 'B' and (resid 49 through 101 )
11X-RAY DIFFRACTION11chain 'B' and (resid 102 through 137 )
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 174 )
13X-RAY DIFFRACTION13chain 'B' and (resid 175 through 210 )

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