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- PDB-7t0i: Crystal structure of S25-39 Fab Unliganded 3 -

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Basic information

Entry
Database: PDB / ID: 7t0i
TitleCrystal structure of S25-39 Fab Unliganded 3
Components
  • S25-39 Fab heavy chain
  • S25-39 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: 2.1 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 20, 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
H: S25-39 Fab heavy chain
L: S25-39 Fab light chain
B: S25-39 Fab heavy chain
A: S25-39 Fab light chain
D: S25-39 Fab heavy chain
C: S25-39 Fab light chain
F: S25-39 Fab heavy chain
E: S25-39 Fab light chain


Theoretical massNumber of molelcules
Total (without water)193,1678
Polymers193,1678
Non-polymers00
Water4,125229
1
H: S25-39 Fab heavy chain
L: S25-39 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,2922
Polymers48,2922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-21 kcal/mol
Surface area19710 Å2
MethodPISA
2
B: S25-39 Fab heavy chain
A: S25-39 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,2922
Polymers48,2922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-20 kcal/mol
Surface area20170 Å2
MethodPISA
3
D: S25-39 Fab heavy chain
C: S25-39 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,2922
Polymers48,2922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-19 kcal/mol
Surface area19500 Å2
MethodPISA
4
F: S25-39 Fab heavy chain
E: S25-39 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,2922
Polymers48,2922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-20 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.555, 111.749, 154.701
Angle α, β, γ (deg.)90.000, 90.050, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody
S25-39 Fab heavy chain


Mass: 24051.963 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
S25-39 Fab light chain


Mass: 24239.896 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.: 229 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M sodium HEPES pH 7.5, 25% PEG MME 2000, 5 mM 4-O-ethoxymethyl-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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.76
11h,-k,-l20.24
ReflectionResolution: 2.1→30 Å / Num. obs: 99437 / % possible obs: 99.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.046 / Rrim(I) all: 0.084 / Χ2: 1.145 / Net I/σ(I): 11.8 / Num. measured all: 328787
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.183.20.38197980.7770.2510.4580.99598.5
2.18-2.263.20.29998830.8520.1960.3591.05699
2.26-2.373.30.25299430.890.1650.3021.09999.6
2.37-2.493.30.20499890.9280.1320.2441.19299.9
2.49-2.653.40.16399750.9520.1050.1941.229100
2.65-2.853.40.12199730.9720.0780.1451.30999.9
2.85-3.143.40.08399870.9860.0540.11.25499.6
3.14-3.593.30.06499840.990.0420.0771.19399.2
3.59-4.523.20.05298650.9930.0350.0631.08698.6
4.52-303.20.045100400.9950.0290.0540.99998.6

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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: 3OKD

3okd


Resolution: 2.1→29.89 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.668 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4905 4.9 %RANDOM
Rwork0.1799 ---
obs0.1821 94531 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.18 Å2 / Biso mean: 43.081 Å2 / Biso min: 17.69 Å2
Baniso -1Baniso -2Baniso -3
1-15.5 Å20 Å28.7 Å2
2---14.62 Å20 Å2
3----0.88 Å2
Refinement stepCycle: final / Resolution: 2.1→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13269 0 0 229 13498
Biso mean---38.22 -
Num. residues----1728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213590
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212429
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.94618470
X-RAY DIFFRACTIONr_angle_other_deg1.102328729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.13751708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.78523.787536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.454152183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6311568
X-RAY DIFFRACTIONr_chiral_restr0.1230.22077
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02115240
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023068
LS refinement shellResolution: 2.101→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 362 -
Rwork0.319 6551 -
all-6913 -
obs--93.55 %

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