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- PDB-5ezl: Crystal Structure of Fab of parasite invasion inhibitory antibody... -

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Basic information

Entry
Database: PDB / ID: 5ezl
TitleCrystal Structure of Fab of parasite invasion inhibitory antibody c1 - monoclinic form
Components(Fab c12) x 2
KeywordsIMMUNE SYSTEM / MALARIA INHIBITORY ANTIBODY / FAB / cyrpa
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsFavuzza, P. / Pluschke, G. / Rudolph, M.G.
CitationJournal: Elife / Year: 2017
Title: Structure of the malaria vaccine candidate antigen CyRPA and its complex with a parasite invasion inhibitory antibody.
Authors: Favuzza, P. / Guffart, E. / Tamborrini, M. / Scherer, B. / Dreyer, A.M. / Rufer, A.C. / Erny, J. / Hoernschemeyer, J. / Thoma, R. / Schmid, G. / Gsell, B. / Lamelas, A. / Benz, J. / Joseph, ...Authors: Favuzza, P. / Guffart, E. / Tamborrini, M. / Scherer, B. / Dreyer, A.M. / Rufer, A.C. / Erny, J. / Hoernschemeyer, J. / Thoma, R. / Schmid, G. / Gsell, B. / Lamelas, A. / Benz, J. / Joseph, C. / Matile, H. / Pluschke, G. / Rudolph, M.G.
History
DepositionNov 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.occupancy / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Fab c12
B: Fab c12
H: Fab c12
L: Fab c12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1616
Polymers94,5154
Non-polymers6462
Water3,423190
1
A: Fab c12
B: Fab c12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6823
Polymers47,2582
Non-polymers4241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-14 kcal/mol
Surface area20320 Å2
MethodPISA
2
H: Fab c12
L: Fab c12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4793
Polymers47,2582
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-19 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.420, 108.900, 97.400
Angle α, β, γ (deg.)90.000, 97.750, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-448-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain H
12chain B
22chain L

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA15 - 251
211chain HH15 - 250
112chain BB25 - 237
212chain LL25 - 237

NCS ensembles :
ID
1
2

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Components

#1: Antibody Fab c12


Mass: 23676.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody Fab c12


Mass: 23581.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES-NaOH pH 7.0, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.43→48.2 Å / Num. obs: 39274 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 48.088 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.148 / Rrim(I) all: 0.176 / Χ2: 0.941 / Net I/σ(I): 7.77 / Num. measured all: 133813
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.43-2.493.51.4110.9910195292429110.3131.66699.6
2.49-2.561.2381.159909286028540.4031.46399.8
2.56-2.641.1011.299208270826880.4471.30699.3
2.64-2.720.8821.598883270526860.5551.05299.3
2.72-2.810.6462.118407260225710.6560.77398.8
2.81-2.90.5422.618575250524780.750.64298.9
2.9-3.010.4163.338477243624110.840.49299
3.01-3.140.3124.398019233423190.9110.37199.4
3.14-3.280.245.767555225322390.950.28699.4
3.28-3.440.1757.426953215221270.9650.20998.8
3.44-3.620.1269.836991205220440.9820.14999.6
3.62-3.840.10911.376717192619120.9870.12999.3
3.84-4.110.08114.666249181418020.9910.09699.3
4.11-4.440.06117.435538170516900.9950.07399.1
4.44-4.860.05220.075270156615530.9960.06299.2
4.86-5.430.05319.94909140613950.9980.06399.2
5.43-6.270.06516.894196125912540.9940.07799.6
6.27-7.680.06117.063531107110660.9950.07399.5
7.68-10.870.03526.9727878248190.9980.04299.4
10.870.02531.4514444684550.9990.0397.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHENIXrefinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ezi, 5ezj

5ezi

5ezj


Resolution: 2.43→48.2 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 1964 5 %
Rwork0.1868 --
obs0.1898 39244 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.02 Å2 / Biso mean: 47.1049 Å2 / Biso min: 19.69 Å2
Refinement stepCycle: final / Resolution: 2.43→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6644 0 42 190 6876
Biso mean--80.3 43.43 -
Num. residues----870
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1992X-RAY DIFFRACTION6.625TORSIONAL
12H1992X-RAY DIFFRACTION6.625TORSIONAL
21B1985X-RAY DIFFRACTION6.625TORSIONAL
22L1985X-RAY DIFFRACTION6.625TORSIONAL
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)
12.5087-1.1217-0.38285.10020.88793.4094-0.0140.09920.07520.1126-0.11120.34350-0.40140.11650.25390.0091-0.0180.3254-0.01160.303919.408233.9488-16.0995
21.3394-0.9704-0.16723.1514-1.06961.532-0.04970.032-0.1440.1275-0.1577-0.1174-0.28040.06780.13060.3263-0.06760.01710.404-0.00790.316329.765219.88583.2821
31.7198-0.4643-0.08381.3501-0.22084.42870.10430.00050.02710.2071-0.0492-0.0213-0.1824-0.0875-0.01010.3664-0.0580.00760.25590.0090.289229.075516.475210.1622
42.6788-0.77280.74412.2211-2.3347.43540.00680.22520.1420.1703-0.3092-0.3962-0.51820.57820.39890.3739-0.05120.00880.33220.00720.426137.71549.669-2.9405
52.94510.41580.67993.44041.17671.8711-0.0416-0.02680.12890.17330.1044-0.0222-0.27120.0725-0.04520.32540.0237-0.01250.26490.01180.331227.430549.5953-4.9562
62.0576-1.32881.41913.7527-0.09442.5217-0.01670.01150.13710.1816-0.2134-0.2658-0.37270.13090.15820.3188-0.0233-0.0090.37760.07980.349342.347323.260413.2324
73.1744-2.49621.16615.4977-0.37032.40680.21560.28940.1032-0.5811-0.16230.00710.04680.4017-0.02220.4849-0.03130.08690.51440.07120.351843.777724.98129.5628
82.8468-1.61271.39482.47840.2753.70490.13260.22560.12020.329-0.3785-0.83060.24670.29080.14750.4349-0.0004-0.02410.42780.09370.403848.209715.387215.4285
92.03070.5385-0.6335.0779-3.03033.80290.101-0.21670.20590.64760.07030.0283-0.434-0.122-0.19620.3372-0.00570.00660.2973-0.0290.288826.636523.614862.106
102.2831-0.0992-0.50213.67170.55085.8171-0.11730.11160.1178-0.15860.252-0.03340.36080.187-0.14610.2468-0.021400.2248-0.00630.301834.921318.451459.2425
117.3315.509-1.61816.5325-5.11456.671-0.1273-0.0061-0.4380.1993-0.4857-0.624-0.11730.51950.59680.29250.0263-0.03010.2137-0.03760.382635.661626.71357.0983
123.75132.6037-1.43985.9427-1.0622.10310.07710.07280.03160.7121-0.01320.005-0.0049-0.2702-0.07980.3005-0.02-0.00360.3127-0.01720.262426.231916.972956.7325
135.52160.29920.65092.83880.30561.1899-0.06120.4578-0.3144-0.3662-0.00960.1573-0.17420.03430.02690.3550.04180.00680.3334-0.03670.297313.290739.093339.0951
143.17960.21681.26793.19430.42732.89690.15550.097-0.3917-0.095-0.11050.2604-0.086-0.2536-0.07620.29830.0364-0.00370.3055-0.0310.40019.598638.225640.489
157.9745-1.84212.5182.2671-0.53853.53730.41480.2629-0.3147-0.5273-0.19850.32430.31370.1915-0.11530.525-0.0082-0.00370.2406-0.03450.345424.43395.728537.5361
162.3688-0.99851.02813.51620.11692.209-0.09550.1732-0.057-0.2230.01210.31620.0565-0.13370.12520.3068-0.0802-0.0270.29250.00120.288723.44652.852748.516
174.0746-0.59332.78253.2286-0.49144.2128-0.35430.1985-0.0658-0.23320.1487-0.0181-0.39490.03250.17510.2951-0.00420.03150.20330.0050.232724.81837.767646.967
186.7597-4.5154.98783.1084-3.47313.84480.7330.0816-0.5161-1.0596-0.16930.86990.3592-0.0273-0.40.47540.0438-0.15790.4436-0.0650.642311.771613.889830.8264
191.89011.61240.3677.2434-0.55842.92670.3010.2757-0.2777-0.0844-0.24570.21480.03980.0165-0.0410.33240.0728-0.03230.4023-0.04030.380511.684635.737828.8594
207.1082.2456-1.94588.0575-0.43388.7978-0.32731.6814-0.8462-1.42450.1705-0.95620.10170.27880.0820.69710.00930.18120.669-0.10240.444516.750836.976316.5867
213.60132.71050.75243.8509-2.13134.2749-0.02610.2669-0.6383-0.51630.1505-0.99360.5655-0.1428-0.09270.56020.1385-0.03940.4648-0.14480.643515.044325.139831.3289
224.641.40920.89782.1298-0.21813.8501-0.28510.73440.2211-1.46620.0858-0.0304-0.1749-0.24560.23130.6094-0.03170.03220.50180.01930.337115.731342.886821.9293
233.43762.65561.18114.7733-0.13822.9423-0.02850.238-0.0206-1.6869-0.12450.96660.1065-0.34670.05520.7135-0.0067-0.13910.6257-0.1030.47586.855734.15118.4694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 119 )A15 - 119
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 154 )A120 - 154
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 236 )A155 - 236
4X-RAY DIFFRACTION4chain 'B' and (resid 25 through 49 )B25 - 49
5X-RAY DIFFRACTION5chain 'B' and (resid 50 through 126 )B50 - 126
6X-RAY DIFFRACTION6chain 'B' and (resid 127 through 174 )B127 - 174
7X-RAY DIFFRACTION7chain 'B' and (resid 175 through 196 )B175 - 196
8X-RAY DIFFRACTION8chain 'B' and (resid 197 through 237 )B197 - 237
9X-RAY DIFFRACTION9chain 'H' and (resid 15 through 47 )H15 - 47
10X-RAY DIFFRACTION10chain 'H' and (resid 48 through 90 )H48 - 90
11X-RAY DIFFRACTION11chain 'H' and (resid 91 through 105 )H91 - 105
12X-RAY DIFFRACTION12chain 'H' and (resid 106 through 131 )H106 - 131
13X-RAY DIFFRACTION13chain 'H' and (resid 132 through 177 )H132 - 177
14X-RAY DIFFRACTION14chain 'H' and (resid 178 through 236 )H178 - 236
15X-RAY DIFFRACTION15chain 'L' and (resid 25 through 42 )L25 - 42
16X-RAY DIFFRACTION16chain 'L' and (resid 43 through 99 )L43 - 99
17X-RAY DIFFRACTION17chain 'L' and (resid 100 through 125 )L100 - 125
18X-RAY DIFFRACTION18chain 'L' and (resid 126 through 137 )L126 - 137
19X-RAY DIFFRACTION19chain 'L' and (resid 138 through 168 )L138 - 168
20X-RAY DIFFRACTION20chain 'L' and (resid 169 through 179 )L169 - 179
21X-RAY DIFFRACTION21chain 'L' and (resid 180 through 198 )L180 - 198
22X-RAY DIFFRACTION22chain 'L' and (resid 199 through 221 )L199 - 221
23X-RAY DIFFRACTION23chain 'L' and (resid 222 through 237 )L222 - 237

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