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- PDB-7t0j: Crystal structure of S25-2 Fab Unliganded 3 -

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Basic information

Entry
Database: PDB / ID: 7t0j
TitleCrystal structure of S25-2 Fab Unliganded 3
Components
  • S25-2 Fab heavy chain
  • S25-2 Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / Fab / Carbohydrate / Induced fit / Conformational selection
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLegg, M.S.G. / Blackler, R.J. / Evans, S.V.
Funding support Austria, 3items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Austria
Austrian Science FundP 24021 Austria
Austrian Science FundP 26919 Austria
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Antigen binding by conformational selection in near-germline antibodies.
Authors: Blackler, R.J. / Muller-Loennies, S. / Pokorny-Lehrer, B. / Legg, M.S.G. / Brade, L. / Brade, H. / Kosma, P. / Evans, S.V.
History
DepositionNov 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: S25-2 Fab light chain
H: S25-2 Fab heavy chain
A: S25-2 Fab light chain
B: S25-2 Fab heavy chain
C: S25-2 Fab light chain
D: S25-2 Fab heavy chain
E: S25-2 Fab light chain
F: S25-2 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)193,7008
Polymers193,7008
Non-polymers00
Water5,116284
1
L: S25-2 Fab light chain
H: S25-2 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)48,4252
Polymers48,4252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-21 kcal/mol
Surface area20220 Å2
MethodPISA
2
A: S25-2 Fab light chain
B: S25-2 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)48,4252
Polymers48,4252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-23 kcal/mol
Surface area19630 Å2
MethodPISA
3
C: S25-2 Fab light chain
D: S25-2 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)48,4252
Polymers48,4252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-24 kcal/mol
Surface area19670 Å2
MethodPISA
4
E: S25-2 Fab light chain
F: S25-2 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)48,4252
Polymers48,4252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-23 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.733, 135.329, 92.667
Angle α, β, γ (deg.)90.000, 94.350, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
S25-2 Fab light chain


Mass: 24242.898 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/c / Description: hybridoma / Production host: Mus musculus (house mouse)
#2: Antibody
S25-2 Fab heavy chain


Mass: 24182.045 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/c / Description: hybridoma / Production host: Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium fluoride, 20% PEG 3350, 5 mM 4-O-methoxymethyl-KdoOMe

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 98548 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.048 / Rrim(I) all: 0.096 / Χ2: 1.078 / Net I/σ(I): 9.7 / Num. measured all: 408414
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.194.10.63449110.7930.3640.7330.796100
2.19-2.234.20.58349340.8230.3330.6730.855100
2.23-2.2740.60148770.8980.3520.6991.30699.6
2.27-2.324.20.5349340.8440.3010.610.90399.9
2.32-2.374.20.4549000.8710.2550.5180.93299.9
2.37-2.424.20.38648990.9020.2170.4440.947100
2.42-2.484.20.32849230.9180.1850.3771.03899.9
2.48-2.554.20.27749320.9390.1560.3181.08599.8
2.55-2.624.30.24749030.9440.1390.2841.12799.9
2.62-2.714.20.22149230.9560.1260.2551.3399.8
2.71-2.814.20.16949230.9760.0950.1951.20699.7
2.81-2.924.20.13848970.9830.0780.1591.24399.8
2.92-3.054.20.11349180.9880.0640.131.26999.7
3.05-3.214.10.09149520.990.0520.1051.33199.8
3.21-3.414.10.07849130.9930.0440.0891.30299.9
3.41-3.6840.0749410.9920.0410.0811.23599.9
3.68-4.0540.05949300.9940.0340.0681.02999.8
4.05-4.6340.04749480.9960.0270.0540.95599.8
4.63-5.834.10.04449650.9960.0250.050.82499.9
5.83-4040.03750250.9980.0210.0430.84899.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q9K

1q9k


Resolution: 2.15→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / SU B: 8.951 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2814 4989 5.1 %RANDOM
Rwork0.2299 ---
obs0.2325 93522 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.46 Å2 / Biso mean: 43.748 Å2 / Biso min: 18.02 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å20 Å2-0.34 Å2
2---3.41 Å20 Å2
3---1.13 Å2
Refinement stepCycle: final / Resolution: 2.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13415 0 0 284 13699
Biso mean---36.19 -
Num. residues----1743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213749
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212522
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.94518696
X-RAY DIFFRACTIONr_angle_other_deg0.948328972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.30951731
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60523.821547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.13152212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4351568
X-RAY DIFFRACTIONr_chiral_restr0.0890.22098
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115446
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023114
LS refinement shellResolution: 2.15→2.202 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.338 379 -
Rwork0.315 6812 -
obs--98.76 %

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