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

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Basic information

Entry
Database: PDB / ID: 5ezj
TitleCrystal Structure of Fab of parasite invasion inhibitory antibody c1 - orthorhombic form
Components
  • Fab c12 Light chain
  • Fab c12 heavy chain
KeywordsIMMUNE SYSTEM / MALARIA INHIBITORY ANTIBODY / FAB / cyrpa
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Structure summary
Revision 1.2Mar 1, 2017Group: Structure summary
Revision 1.3Apr 26, 2017Group: Other / 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 / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab c12 heavy chain
B: Fab c12 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9463
Polymers47,2142
Non-polymers7331
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-9 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.810, 72.770, 109.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab c12 heavy chain


Mass: 23632.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#2: Antibody Fab c12 Light chain


Mass: 23581.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.74 Å3/Da / Density % sol: 55.19 %
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: 0.99993 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99993 Å / Relative weight: 1
ReflectionResolution: 1.89→41.9 Å / Num. obs: 41941 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 45.83 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.131 / Χ2: 1.024 / Net I/σ(I): 8.71 / Num. measured all: 262881
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.89-1.946.71.921.0516595311127040.6742.10186.9
1.94-1.994.070.7519866300730070.4944.421100
1.99-2.051.5141.6119736291129100.6551.641100
2.05-2.111.1552.0719128284628460.8021.254100
2.11-2.181.0852.3618278277327720.8091.179100
2.18-2.260.7982.9916813269326610.8550.87298.8
2.26-2.340.9372.9615361257925540.891.02899
2.34-2.440.4485.1416267250625060.9480.488100
2.44-2.550.3226.9315493236723660.9680.351100
2.55-2.670.2418.614775231123090.9810.26499.9
2.67-2.820.17310.9913521219221900.9870.1999.9
2.82-2.990.13512.9911834207020690.9880.149100
2.99-3.190.10316.2211597196819670.990.11499.9
3.19-3.450.0918.5511026182818260.9940.09999.9
3.45-3.780.08918.9110070169216900.9920.09899.9
3.78-4.230.07321.748706153415330.9940.0899.9
4.23-4.880.06323.487908138013760.9960.06999.7
4.88-5.980.06224.47274115911590.9950.068100
5.98-8.450.05423.2654049389370.9970.05999.9
8.450.04325.1432295675590.9950.04898.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ezi

5ezi


Resolution: 1.95→41.915 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2468 1902 5.01 %
Rwork0.1981 --
obs0.2006 37950 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→41.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 49 255 3624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073466
X-RAY DIFFRACTIONf_angle_d0.9014733
X-RAY DIFFRACTIONf_dihedral_angle_d15.0172064
X-RAY DIFFRACTIONf_chiral_restr0.052542
X-RAY DIFFRACTIONf_plane_restr0.006596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99880.44631330.3912385X-RAY DIFFRACTION92
1.9988-2.05280.38081200.30992563X-RAY DIFFRACTION100
2.0528-2.11320.33031360.29962568X-RAY DIFFRACTION100
2.1132-2.18140.34591400.30762590X-RAY DIFFRACTION100
2.1814-2.25940.52441240.44882315X-RAY DIFFRACTION89
2.2594-2.34990.37771140.33982489X-RAY DIFFRACTION96
2.3499-2.45680.34531470.25382583X-RAY DIFFRACTION100
2.4568-2.58630.31141340.22532617X-RAY DIFFRACTION100
2.5863-2.74830.28181270.20892602X-RAY DIFFRACTION100
2.7483-2.96050.26471390.21032617X-RAY DIFFRACTION100
2.9605-3.25830.2081520.18982623X-RAY DIFFRACTION100
3.2583-3.72950.22931650.18262604X-RAY DIFFRACTION100
3.7295-4.69780.19011340.14112679X-RAY DIFFRACTION100
4.6978-41.92460.1861370.14042813X-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)
12.12690.5889-1.50611.663-0.78984.076-0.0907-0.00120.12370.01450.0772-0.0101-0.0262-0.02520.01130.22210.0119-0.01090.2402-0.03490.31912.322515.2996-4.7455
28.2816-0.8755-2.520.24211.03929.467-0.30640.1198-0.76910.25110.25830.15341.4288-0.08060.0730.42730.0055-0.06920.35070.07120.415118.0249-21.690316.4687
34.1208-2.28980.02596.20880.3625.40090.27930.1845-0.03-0.1878-0.1079-0.24920.05380.079-0.19080.2690.03550.04510.3030.04050.242418.2258-10.48312.4776
41.63350.84340.49923.9123-0.0974.34680.11060.122-0.1611-0.04940.037-0.01530.4209-0.0311-0.12790.27180.0146-0.06740.2675-0.04840.271110.4481.1173-21.2582
50.3329-1.26921.05965.4969-4.24193.30960.2778-0.4997-0.0731-1.23990.06720.50430.7227-0.0699-0.40030.8146-0.0235-0.10140.4886-0.03710.437610.6004-19.0779-10.768
61.22450.36090.07262.22571.05448.07080.24630.0951-0.1461-0.1168-0.08280.3650.2442-0.9217-0.13230.3202-0.0091-0.0920.49130.03020.40887.3608-19.38637.6157
72.8356-0.339-1.41617.44624.44653.24910.07620.0661-0.25360.3003-0.23350.5720.7284-1.10950.21030.3698-0.1131-0.06480.52450.0880.46834.5795-25.356714.4268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 139 )
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 154 )
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 236 )
4X-RAY DIFFRACTION4chain 'B' and (resid 25 through 126 )
5X-RAY DIFFRACTION5chain 'B' and (resid 127 through 137 )
6X-RAY DIFFRACTION6chain 'B' and (resid 138 through 198 )
7X-RAY DIFFRACTION7chain 'B' and (resid 199 through 237 )

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