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- PDB-6ule: Crystal structure of 2541 Fab in complex with circumsporozoite pr... -

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Basic information

Entry
Database: PDB / ID: 6ule
TitleCrystal structure of 2541 Fab in complex with circumsporozoite protein NANP5
Components
  • 2541 Antibody, heavy chain
  • 2541 Antibody, light chain
  • Circumsporozoite protein
KeywordsIMMUNE SYSTEM / Malaria / 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: 2.55 Å
AuthorsThai, E. / Scally, S.W. / Murugan, R. / Wardemann, H. / Julien, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1179906; J.-P.J. United States
CitationJournal: Nat. Med. / Year: 2020
Title: Evolution of protective human antibodies against Plasmodium falciparum circumsporozoite protein repeat motifs.
Authors: Murugan, R. / Scally, S.W. / Costa, G. / Mustafa, G. / Thai, E. / Decker, T. / Bosch, A. / Prieto, K. / Levashina, E.A. / Julien, J.P. / Wardemann, H.
History
DepositionOct 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2541 Antibody, heavy chain
B: 2541 Antibody, light chain
C: 2541 Antibody, heavy chain
D: 2541 Antibody, light chain
I: Circumsporozoite protein


Theoretical massNumber of molelcules
Total (without water)97,4175
Polymers97,4175
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-59 kcal/mol
Surface area39380 Å2
Unit cell
Length a, b, c (Å)66.770, 63.694, 146.654
Angle α, β, γ (deg.)90.000, 100.997, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody 2541 Antibody, heavy chain


Mass: 24263.318 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 2541 Antibody, light chain


Mass: 23444.930 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: Protein/peptide Circumsporozoite protein / / CS


Mass: 2000.006 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.17 Å3/Da / Density % sol: 61.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1.8 M ammonium sulfate, 0.1 M citric acid pH 3.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.55→40 Å / Num. obs: 39583 / % possible obs: 99.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 69.82 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.039 / Net I/σ(I): 13.8
Reflection shellResolution: 2.55→2.59 Å / Rmerge(I) obs: 0.749 / Num. unique obs: 1755 / CC1/2: 0.701

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D01
Resolution: 2.55→38.33 Å / SU ML: 0.4834 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.6839
RfactorNum. reflection% reflection
Rfree0.2588 1976 5 %
Rwork0.2085 --
obs0.211 39506 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 86.62 Å2
Refinement stepCycle: LAST / Resolution: 2.55→38.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6746 0 0 93 6839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026955
X-RAY DIFFRACTIONf_angle_d0.50579486
X-RAY DIFFRACTIONf_chiral_restr0.04111065
X-RAY DIFFRACTIONf_plane_restr0.00381212
X-RAY DIFFRACTIONf_dihedral_angle_d13.30854160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.41171330.35812621X-RAY DIFFRACTION98.39
2.61-2.680.40411360.34842640X-RAY DIFFRACTION98.75
2.68-2.760.31761440.32682648X-RAY DIFFRACTION98.62
2.76-2.850.38491430.30872642X-RAY DIFFRACTION99.04
2.85-2.950.39651350.32432654X-RAY DIFFRACTION98.94
2.95-3.070.40061470.31232685X-RAY DIFFRACTION99.09
3.07-3.210.40521420.2912665X-RAY DIFFRACTION99.5
3.21-3.380.28471430.24732677X-RAY DIFFRACTION99.58
3.38-3.590.27961380.21342676X-RAY DIFFRACTION99.58
3.59-3.870.23171390.20072683X-RAY DIFFRACTION99.61
3.87-4.260.21681400.16132703X-RAY DIFFRACTION99.48
4.26-4.880.18771450.14042714X-RAY DIFFRACTION99.86
4.88-6.140.21381440.1732734X-RAY DIFFRACTION99.76
6.14-38.330.23731470.19792788X-RAY DIFFRACTION99.63
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)
11.773750204780.331660086558-0.08819403837695.07208856601-4.200002364655.524143244040.30700784703-0.609429480171-0.1421849107810.683466697029-0.674308602349-0.691563744424-0.5346526768050.7600569749880.332484745010.815117466435-0.186175962895-0.0213750953350.6554375333760.1062449176020.5619459257369.9994142005418.458917224631.0292178048
28.74154557916-2.467119412661.161232428364.17411933565-0.7371515949682.42606097807-0.29026236026-0.1165426458580.3012231968530.1079907160790.0156168176435-0.0502224571959-0.380866757491-0.08920069601570.2416548952640.9155578979749.25611614305E-50.1785010574420.3808572334510.03383248607470.474896009925-4.203120402742.22313589888.14879670099
36.14526662156-2.020650622951.087943217074.50281245542-0.9912308869883.101033331970.307488644571-0.47841307275-0.2835221651740.3023548705070.02461107342340.2886803970650.143010027494-0.718698231306-0.3176639354280.768881945558-0.08322232236440.09076696981690.6529418594750.1127906779230.457310278207-11.142283186312.464938992730.2946213435
45.91885066581-0.111775731206-1.272715203141.63068330134-0.06521629132125.05528529290.15360669388-0.0629178651281-0.0175869335891-0.3295994429170.008122824742760.0408295128603-0.346623151048-0.11830854317-0.158633772480.9138994058350.03163587729570.1621549893560.3528225497260.08221046667660.554463394137-10.072866991629.68836724550.709652309014
51.781937825551.082362629660.8541039821923.156223858051.906220333974.212223269540.0671690416359-0.0947373366629-0.0592730421729-0.000643139391314-0.0858653207993-0.180906231091-0.1256961995880.0122480736485-0.001276741403560.540808960945-0.04149029494540.1020695895150.5219954033370.1160438559590.52397116858612.38320409912.0194910309371.1307204319
63.994941938282.98362397687-4.632937938674.32633698444-3.773620346485.090410306410.0492497719423-0.222700605540.1747385158330.6479973977180.1005451630210.316519682038-0.333700135389-0.117510449917-0.0957209165840.923215145888-0.1942293469420.2129832190721.12451240632-0.1213626150320.6348197596321.371380165055.95223323546104.980390704
77.044455177010.249510528956-0.5946310598174.148344555261.474779960128.396476020040.094051702133-0.5968806277470.1132780184510.106403031688-0.293031470070.952585033047-0.0174354553505-1.990795025220.169108786450.463119060094-0.0107822232060.01166658092270.9259938494760.01713215303090.657686184506-9.34116970419-0.21908130089868.8920645115
82.208337719371.233964341210.9107866643643.248772255460.7034945174781.08517161468-0.0320352190033-0.1384588319540.2690022655430.373697987519-0.3683601015330.5950347651890.0999557664364-1.043939160010.3591381752190.984859453508-0.04879610584870.2579673487521.46021927876-0.1504056066780.780983780499-8.9384466699716.977783277199.4822959536
92.861131600340.9861490013890.6406959893291.22618160726-2.093594959997.99834034538-0.3340704748210.3226631176290.145800781368-1.181639630030.4885011260890.23988010476-0.3794516878360.131524262341-0.160284494510.867261447968-0.1173728388880.0283021687760.6975358628410.07707711635550.5632609157697.390396217270.83574611701947.5483785159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and resid 1 through 123A0
2X-RAY DIFFRACTION2chain 'A' and resid 124 through 225A0
3X-RAY DIFFRACTION3chain 'B' and resid 1 through 106B0
4X-RAY DIFFRACTION4chain 'B' and resid 107 through 213B0
5X-RAY DIFFRACTION5chain 'C' and resid 1 through 123C0
6X-RAY DIFFRACTION6chain 'C' and resid 124 through 224C0
7X-RAY DIFFRACTION7chain 'D' and resid 1 through 106D0
8X-RAY DIFFRACTION8chain 'D' and resid 107 through 213D0
9X-RAY DIFFRACTION9chain 'I'I3 - 19

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