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- PDB-5szf: 2A10 FAB fragment 2.54 Angstoms -

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Basic information

Entry
Database: PDB / ID: 5szf
Title2A10 FAB fragment 2.54 Angstoms
Components
  • 2A10 antibody FAB fragment heavy chain
  • 2A10 antibody FAB fragment light chain
KeywordsIMMUNE SYSTEM / Malaria Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.52 Å
AuthorsJackson, C.J. / Fisher, C.
CitationJournal: PLoS Pathog. / Year: 2017
Title: T-dependent B cell responses to Plasmodium induce antibodies that form a high-avidity multivalent complex with the circumsporozoite protein.
Authors: Fisher, C.R. / Sutton, H.J. / Kaczmarski, J.A. / McNamara, H.A. / Clifton, B. / Mitchell, J. / Cai, Y. / Dups, J.N. / D'Arcy, N.J. / Singh, M. / Chuah, A. / Peat, T.S. / Jackson, C.J. / Cockburn, I.A.
History
DepositionAug 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _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_author.name
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature
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
L: 2A10 antibody FAB fragment light chain
H: 2A10 antibody FAB fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5366
Polymers47,1512
Non-polymers3844
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-63 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.213, 204.213, 204.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11H-424-

HOH

DetailsDimer confirmed by size exclusion chromatography

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Components

#1: Antibody 2A10 antibody FAB fragment light chain


Mass: 23457.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 2A10 antibody FAB fragment heavy chain


Mass: 23693.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.8 Å3/Da / Density % sol: 67.6 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 2M Ammonium sulfate 0.1 M trisodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.52→39.2 Å / Num. obs: 24796 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0245 / Net I/σ(I): 24.1
Reflection shellLowest resolution: 2.52 Å / Redundancy: 2.61 % / Rmerge(I) obs: 0.3658

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.52→37.284 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 1228 4.95 %
Rwork0.2251 --
obs0.2263 24796 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.52→37.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 20 46 3354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033387
X-RAY DIFFRACTIONf_angle_d0.5684608
X-RAY DIFFRACTIONf_dihedral_angle_d9.8281193
X-RAY DIFFRACTIONf_chiral_restr0.028518
X-RAY DIFFRACTIONf_plane_restr0.004581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5202-2.62110.32411210.33192593X-RAY DIFFRACTION100
2.6211-2.74030.32141320.31082567X-RAY DIFFRACTION100
2.7403-2.88470.2831380.29062575X-RAY DIFFRACTION100
2.8847-3.06540.33111540.28362554X-RAY DIFFRACTION100
3.0654-3.3020.31891180.26942618X-RAY DIFFRACTION100
3.302-3.6340.28531160.23752621X-RAY DIFFRACTION100
3.634-4.15920.22691480.20012605X-RAY DIFFRACTION100
4.1592-5.23790.18821500.16832648X-RAY DIFFRACTION100
5.2379-37.28810.21381510.19452787X-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)
10.99920.20110.53089.7503-9.56579.93510.57510.9724-0.209-1.5014-0.0730.65260.182-0.5532-0.54161.25490.474-0.12610.8583-0.01350.487618.9168-28.9835-10.212
22.15350.5236-1.12550.9541-0.2241.01520.31760.33610.3305-0.1131-0.5269-0.44490.28510.40740.03360.84660.51390.25740.8220.17970.447727.111-23.4819-2.2609
32.8872-0.9728-2.00622.10410.23771.52150.46830.3849-0.4532-0.967-0.479-0.07450.09340.13280.16551.27520.58610.14310.86540.09780.481729.5627-29.3634-10.6833
40.81820.33140.90410.7708-0.32092.38190.45740.35110.1196-0.8492-0.0926-0.06950.01080.1086-0.2680.94970.43090.11660.69560.09790.475923.2495-24.3798-6.0629
53.4561-2.3211-1.1544.46921.24061.9690.00890.4757-0.47720.79510.06191.34630.1638-0.1733-0.09990.73710.20310.18250.38110.17110.7865.1309-32.180918.7734
61.2418-0.65980.04180.48470.5750.89560.94480.6164-0.29620.98190.5441.5295-0.311-0.2213-0.43661.00260.03210.95510.24580.61391.5836-5.7493-31.707224.4683
71.6836-1.9101-0.6367.75622.16441.70260.2019-0.018-0.6480.34880.48781.0308-0.2867-0.0594-0.05441.49790.10140.8860.28490.31231.5809-3.8574-38.944426.5877
80.3935-0.48440.05991.3735-0.0492.3139-0.09060.23660.05990.169-0.2431-0.39110.28080.90930.28260.61840.38560.23160.79890.31170.570224.9457-7.04061.8862
91.408-0.0233-1.24581.0935-0.64462.1094-0.09290.3004-0.03920.0621-0.3033-0.35770.47310.55420.360.60350.31120.22320.75330.29880.528721.1635-5.8381.3327
102.4444-0.45570.23274.8533-2.30633.6438-0.19-0.2547-0.43681.33690.4058-0.19740.0638-0.023-0.23050.83550.2183-0.01880.43440.15930.55412.2662-25.804126.1888
113.24751.597-0.6838.3244-5.48323.95740.0315-0.8048-0.1721.63580.02980.06440.25220.39390.09681.31360.2412-0.07880.59740.12010.567615.4452-25.242435.2811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 32 )
2X-RAY DIFFRACTION2chain 'L' and (resid 33 through 49 )
3X-RAY DIFFRACTION3chain 'L' and (resid 50 through 75 )
4X-RAY DIFFRACTION4chain 'L' and (resid 76 through 102 )
5X-RAY DIFFRACTION5chain 'L' and (resid 103 through 181 )
6X-RAY DIFFRACTION6chain 'L' and (resid 182 through 201 )
7X-RAY DIFFRACTION7chain 'L' and (resid 202 through 214 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 51 )
9X-RAY DIFFRACTION9chain 'H' and (resid 52 through 126 )
10X-RAY DIFFRACTION10chain 'H' and (resid 127 through 189 )
11X-RAY DIFFRACTION11chain 'H' and (resid 190 through 220 )

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