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- PDB-8rel: Fab of an anti-PvAMA1 monoclonal antibody -

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Basic information

Entry
Database: PDB / ID: 8rel
TitleFab of an anti-PvAMA1 monoclonal antibody
Components
  • Fab 8.1.1 heavy chain
  • Fab 8.1.1 light chain
KeywordsIMMUNE SYSTEM / monoclonal antobody / anti-AMA-1 / Fab
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBentley, G.A. / Saul, F.A. / Vulliez-LeNormand, B.
Funding support France, 1items
OrganizationGrant numberCountry
Other private France
CitationJournal: J Struct Biol X / Year: 2024
Title: Conformational variability in the D2 loop of Plasmodium Apical Membrane antigen 1.
Authors: Saul, F.A. / Vulliez-Le Normand, B. / Boes, A. / Spiegel, H. / Kocken, C.H.M. / Faber, B.W. / Bentley, G.A.
History
DepositionDec 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab 8.1.1 heavy chain
L: Fab 8.1.1 light chain
M: Fab 8.1.1 heavy chain
N: Fab 8.1.1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7075
Polymers93,6724
Non-polymers351
Water7,891438
1
H: Fab 8.1.1 heavy chain
L: Fab 8.1.1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8713
Polymers46,8362
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-36 kcal/mol
Surface area18590 Å2
2
M: Fab 8.1.1 heavy chain
N: Fab 8.1.1 light chain


Theoretical massNumber of molelcules
Total (without water)46,8362
Polymers46,8362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-22 kcal/mol
Surface area18450 Å2
Unit cell
Length a, b, c (Å)53.490, 61.520, 116.990
Angle α, β, γ (deg.)90.00, 97.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab 8.1.1 heavy chain


Mass: 23539.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab 8.1.1 light chain


Mass: 23296.701 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: Crystals of Fab8.1.1 were obtained by mixing 1 micro-L of protein and 1 micro-L of reservoir containing 24% PEG 4000, 80 mM sodium acetate pH 4.6 and 0.16 M ammonium acetate. The final ...Details: Crystals of Fab8.1.1 were obtained by mixing 1 micro-L of protein and 1 micro-L of reservoir containing 24% PEG 4000, 80 mM sodium acetate pH 4.6 and 0.16 M ammonium acetate. The final protein concentration was 3.6 mg/ml. Cryo-protecting buffer for FabF8.1.1 consisted of the crystallisation buffer where PEG was increased to 30% added with 15% of glycerol (v/v).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 4, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.1→46.02 Å / Num. obs: 41875 / % possible obs: 94.8 % / Redundancy: 3.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.083 / Rrim(I) all: 0.162 / Net I/σ(I): 7.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4784 / CC1/2: 0.503 / Rpim(I) all: 0.369 / Rrim(I) all: 0.713 / % possible all: 74.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.24 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 16.307 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25461 1231 2.9 %RANDOM
Rwork0.20035 ---
obs0.20206 40631 94.57 %-
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: 30.766 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20.03 Å2
2--0.71 Å20 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 2.1→42.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6344 0 1 438 6783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0126515
X-RAY DIFFRACTIONr_bond_other_d0.0040.0165856
X-RAY DIFFRACTIONr_angle_refined_deg1.0651.6638879
X-RAY DIFFRACTIONr_angle_other_deg0.3861.57213580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.069527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85101007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0520.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027589
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021459
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4372.4413318
X-RAY DIFFRACTIONr_mcbond_other1.4362.4413318
X-RAY DIFFRACTIONr_mcangle_it2.4194.3784130
X-RAY DIFFRACTIONr_mcangle_other2.4194.3774131
X-RAY DIFFRACTIONr_scbond_it1.5492.6263197
X-RAY DIFFRACTIONr_scbond_other1.5472.6263196
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5874.7424750
X-RAY DIFFRACTIONr_long_range_B_refined5.09528.657085
X-RAY DIFFRACTIONr_long_range_B_other5.01828.197011
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 65 -
Rwork0.307 2137 -
obs--68.03 %
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)
11.30860.0130.29770.1113-0.04340.2004-0.01530.0252-0.001-0.0380.0184-0.0286-0.0177-0.0359-0.0030.0511-0.0003-0.020.1007-0.00120.046919.9457-3.6809-11.3549
20.9734-0.2093-0.12930.0626-0.04010.45740.0477-0.06630.0278-0.0147-0.01920.00320.0070.0335-0.02850.0187-0.0113-0.02180.1544-0.00290.035310.1338-4.557620.3068
31.7525-0.1410.5670.1043-0.16880.66220.0376-0.20880.00240.01080.0011-0.001-0.0063-0.1317-0.03870.0045-0.02290.00030.20840.00760.005327.7647-4.307271.6663
40.64410.2001-0.060.1822-0.02370.9327-0.0207-0.0719-0.0396-0.03-0.0019-0.00280.0111-0.07760.02260.00940.0113-0.00590.2035-0.00230.012237.3311-3.240539.7986
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 114
2X-RAY DIFFRACTION1L1 - 107
3X-RAY DIFFRACTION2H115 - 213
4X-RAY DIFFRACTION2L108 - 213
5X-RAY DIFFRACTION3M1 - 114
6X-RAY DIFFRACTION3N2 - 107
7X-RAY DIFFRACTION4M115 - 213
8X-RAY DIFFRACTION4N108 - 213

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