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- PDB-7t0g: Crystal structure of S25-39 Fab Unliganded 1 -

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Basic information

Entry
Database: PDB / ID: 7t0g
TitleCrystal structure of S25-39 Fab Unliganded 1
Components
  • S25-39 Fab heavy chain
  • S25-39 Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / Fab / Carbohydrate / Induced fit / Conformational selection
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: S25-39 Fab heavy chain
L: S25-39 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5013
Polymers48,2922
Non-polymers2091
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-18 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.610, 61.218, 63.573
Angle α, β, γ (deg.)90.000, 98.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody S25-39 Fab heavy chain


Mass: 24051.963 Da / Num. of mol.: 1
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.: 1
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: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M BIS-TRIS pH 6.5, 20% PEG MME 2000, 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: 1.53→50 Å / Num. obs: 59940 / % possible obs: 99.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.044 / Rrim(I) all: 0.118 / Χ2: 0.947 / Net I/σ(I): 9.3 / Num. measured all: 393256
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.53-1.564.10.61226080.7060.3230.6950.7386.4
1.56-1.584.90.62330360.8520.3020.6940.745100
1.58-1.625.20.60829470.8810.2870.6740.724100
1.62-1.655.50.67230230.8630.3080.7410.774100
1.65-1.685.80.66230090.8820.2920.7250.77100
1.68-1.726.10.6529950.8960.280.7090.801100
1.72-1.776.30.62230280.910.260.6750.848100
1.77-1.816.70.57730040.9490.2360.6250.877100
1.81-1.876.90.51529780.9630.2080.5560.938100
1.87-1.937.10.42830290.9680.1710.4611.04100
1.93-27.20.34129960.9780.1360.3681.11100
2-2.087.30.28230010.9850.1120.3041.188100
2.08-2.177.30.23930270.9850.0960.2571.202100
2.17-2.297.40.19930180.9870.0790.2141.174100
2.29-2.437.50.16229970.990.0640.1751.089100
2.43-2.627.40.12930400.9930.0510.1391.026100
2.62-2.887.30.10230310.9940.0410.111.088100
2.88-3.37.20.07230290.9960.0290.0770.97599.9
3.3-4.1570.05430400.9970.0220.0580.899.8
4.15-506.90.04431040.9970.0180.0480.59199.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OKD

3okd


Resolution: 1.53→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.554 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 2811 4.9 %RANDOM
Rwork0.1761 ---
obs0.1778 54703 95.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.27 Å2 / Biso mean: 15.279 Å2 / Biso min: 4.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0.12 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.53→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 14 474 3828
Biso mean--19.43 23.97 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.023521
X-RAY DIFFRACTIONr_bond_other_d0.0010.023200
X-RAY DIFFRACTIONr_angle_refined_deg2.1791.9494785
X-RAY DIFFRACTIONr_angle_other_deg0.97737412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1025443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.15923.841138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59615566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3151517
X-RAY DIFFRACTIONr_chiral_restr0.1510.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213941
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02790
LS refinement shellResolution: 1.533→1.572 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 140 -
Rwork0.201 2751 -
all-2891 -
obs--65.67 %

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