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- PDB-1z3g: Crystal structure of complex between Pvs25 and Fab fragment of ma... -

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Basic information

Entry
Database: PDB / ID: 1z3g
TitleCrystal structure of complex between Pvs25 and Fab fragment of malaria transmission blocking antibody 2A8
Components
  • 2A8 Fab Heavy Chain
  • 2A8 Fab Light Chain
  • ookinete surface protein Pvs25
KeywordsIMMUNE SYSTEM/CELL ADHESION / 2A8 Fab / Pvs25 / IMMUNE SYSTEM-CELL ADHESION COMPLEX
Function / homology
Function and homology information


calcium ion binding / cell surface / membrane
Similarity search - Function
Plasmodium vivax P25 fold / Plasmodium vivax P25 domain / Ookinete surface antigen, EGF domain / Pvs28 EGF domain / Orthogonal Prism / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. ...Plasmodium vivax P25 fold / Plasmodium vivax P25 domain / Ookinete surface antigen, EGF domain / Pvs28 EGF domain / Orthogonal Prism / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ookinete surface protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Plasmodium vivax SaI-1 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSaxena, A.K. / Singh, K. / Su, H.P. / Klein, M.M. / Stowers, A.W. / Saul, A.J. / Long, C.A. / Garboczi, D.N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: The essential mosquito-stage P25 and P28 proteins from Plasmodium form tile-like triangular prisms
Authors: Saxena, A.K. / Singh, K. / Su, H.P. / Klein, M.M. / Stowers, A.W. / Saul, A.J. / Long, C.A. / Garboczi, D.N.
History
DepositionMar 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Apr 3, 2024Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Remark 999SEQUENCE The sequence of 2A8 FAB Light chain and Heavy chain are not available in any database

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 2A8 Fab Light Chain
H: 2A8 Fab Heavy Chain
M: 2A8 Fab Light Chain
I: 2A8 Fab Heavy Chain
A: ookinete surface protein Pvs25
B: ookinete surface protein Pvs25


Theoretical massNumber of molelcules
Total (without water)134,2126
Polymers134,2126
Non-polymers00
Water0
1
L: 2A8 Fab Light Chain
H: 2A8 Fab Heavy Chain
A: ookinete surface protein Pvs25


Theoretical massNumber of molelcules
Total (without water)67,1063
Polymers67,1063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: 2A8 Fab Light Chain
I: 2A8 Fab Heavy Chain
B: ookinete surface protein Pvs25


Theoretical massNumber of molelcules
Total (without water)67,1063
Polymers67,1063
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.262, 61.649, 142.650
Angle α, β, γ (deg.)90.00, 101.68, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21M
12L
22M
13H
23I
14H
24I
15A
25B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNASNASNLA1 - 1061 - 106
21GLNGLNASNASNMC1 - 1061 - 106
12ARGARGCYSCYSLA107 - 213107 - 213
22ARGARGCYSCYSMC107 - 213107 - 213
13GLNGLNSERSERHB3 - 1143 - 114
23GLNGLNSERSERID3 - 1143 - 114
14ALAALAASPASPHB115 - 216115 - 216
24ALAALAASPASPID115 - 216115 - 216
15ALAALALEULEUAE1 - 1736 - 178
25ALAALALEULEUBF1 - 1736 - 178

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Antibody 2A8 Fab Light Chain


Mass: 23328.637 Da / Num. of mol.: 2 / Fragment: Fab Light Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma / Production host: Mus musculus (house mouse)
#2: Antibody 2A8 Fab Heavy Chain


Mass: 23229.127 Da / Num. of mol.: 2 / Fragment: Fab Heavy Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma / Production host: Mus musculus (house mouse)
#3: Protein ookinete surface protein Pvs25


Mass: 20548.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax SaI-1 (eukaryote) / Species: Plasmodium vivax / Strain: SalI / Plasmid: YEpRPEU-3 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): VK1 / Keywords: P. vivax ookinete surface protein, Pvs25 / References: UniProt: O96555

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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: 2.78 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG6000, Lithium Chloride, Citic acid buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97942 / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 3.3→49.16 Å / Num. all: 21703 / Num. obs: 21703 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 34.2 Å2 / Rsym value: 0.275 / Χ2: 0.87 / Net I/σ(I): 5.2
Reflection shellResolution: 3.3→3.36 Å / % possible obs: 87.5 % / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.3 / Num. measured obs: 974 / Num. unique all: 21703 / Rsym value: 0.01 / Χ2: 0.771 / % possible all: 87.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.6data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Pvs25 model, 2E8 Fab model

Resolution: 3.3→49.15 Å / Cor.coef. Fo:Fc: 0.842 / Cor.coef. Fo:Fc free: 0.784 / SU B: 88.4 / SU ML: 0.65 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.74 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.327 1095 5 %RANDOM
Rwork0.272 ---
all0.275 21703 --
obs0.275 20602 94.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å2-4.09 Å2
2---5.31 Å20 Å2
3---2.16 Å2
Refinement stepCycle: LAST / Resolution: 3.3→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9120 0 0 0 9120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229349
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.94712714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98751194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.91525.707368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.446151562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4821518
X-RAY DIFFRACTIONr_chiral_restr0.0960.21416
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026974
X-RAY DIFFRACTIONr_nbd_refined0.2740.24262
X-RAY DIFFRACTIONr_nbtor_refined0.3130.26248
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2302
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3350.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.212
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: medium positional / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A7950.26
2A8390.36
3B8720.33
4B7450.77
5A13090.54
LS refinement shellResolution: 3.3→3.368 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 73 -
Rwork0.344 1359 -
obs-1359 85.85 %
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)
14.639-0.07381.37025.5601-0.37044.4980.1394-0.12930.54860.0583-0.1457-0.4701-0.01570.12360.0063-0.3811-0.03330.0697-0.2379-0.0149-0.234378.3771-7.0229-4.3366
211.28290.72670.35114.8075-0.5533.00950.0247-0.25590.79430.1398-0.0574-0.3348-0.1894-0.23530.0327-0.05960.04410.0048-0.3318-0.0274-0.308345.07097.8704-13.0242
39.6327-0.9831-1.10612.6303-0.48422.49170.2046-0.0297-0.1106-0.1096-0.0085-0.15410.0465-0.1147-0.196-0.23-0.0434-0.016-0.4197-0.0033-0.475267.3447-26.3707-9.6759
43.22560.62711.38315.0268-1.55075.9590.05460.20790.2011-0.5411-0.01770.17-0.498-0.2088-0.037-0.29610.01340.1024-0.1297-0.0962-0.296447.7786-4.3672-23.0332
51.3306-1.7172-2.19925.23264.87225.3015-0.02340.42850.0311-0.3950.1512-0.0315-0.07710.044-0.1278-0.11710.0305-0.04290.08170.0075-0.1589.7205-47.2111-31.3832
66.23-0.67832.30448.2129-0.66794.9207-0.0598-0.0585-0.0483-0.03870.0481-0.06840.413-0.0450.01180.0238-0.0349-0.0435-0.2205-0.0337-0.521119.1468-22.5524-61.4968
72.93470.77850.77433.82633.46049.31530.027-0.4585-0.27270.2004-0.1790.12550.1957-0.05630.152-0.09640.0244-0.0263-0.10450.1338-0.038326.8108-35.0023-26.3106
81.4913-0.6447-0.37673.0214-1.31267.8339-0.0033-0.19980.08420.09290.0695-0.3184-0.00780.0987-0.0662-0.16610.0439-0.0179-0.3375-0.0531-0.353724.5692-2.6708-51.5483
94.6751-1.58480.42157.4766-0.29993.09240.0579-0.0777-0.4635-0.4003-0.0035-0.15250.16050.1369-0.0544-0.0145-0.07770.0087-0.1484-0.0054-0.386137.8982-24.3318-30.5264
104.2792.627-1.04184.0346-1.13381.6445-0.0380.22140.3004-0.57570.1396-1.1194-0.39730.7637-0.10160.374-0.05910.23550.3569-0.07970.297145.324517.4041-75.3562
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LA1 - 1061 - 106
22LA107 - 213107 - 213
33HB3 - 1143 - 114
44HB115 - 216115 - 216
55AE1 - 1736 - 178
66MC1 - 1061 - 106
77MC107 - 213107 - 213
88ID3 - 1143 - 114
99ID115 - 216115 - 216
1010BF1 - 1736 - 178

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