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- PDB-7t0h: Crystal structure of S25-39 Fab Unliganded 2 -

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Basic information

Entry
Database: PDB / ID: 7t0h
TitleCrystal structure of S25-39 Fab Unliganded 2
Components
  • S25-39 Fab heavy chain
  • S25-39 Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / Fab / Carbohydrate / Induced fit / Conformational selection
Function / homologyBROMIDE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)48,6917
Polymers48,2922
Non-polymers4005
Water10,647591
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-21 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.593, 63.135, 61.885
Angle α, β, γ (deg.)90.000, 99.360, 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-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Potassium Bromide, 30% 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: 1.3→40 Å / Num. obs: 103442 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.036 / Rrim(I) all: 0.067 / Χ2: 0.91 / Net I/σ(I): 13 / Num. measured all: 380775
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.3-1.323.70.54751630.8070.3310.6410.75799.4
1.32-1.353.70.48751010.8470.2940.570.7999.5
1.35-1.373.70.40451670.8810.2440.4730.78299.6
1.37-1.43.70.34451690.9120.2080.4030.8199.7
1.4-1.433.70.29451730.9330.1770.3440.82199.8
1.43-1.463.70.25151900.9460.1510.2940.83199.8
1.46-1.53.70.21151930.9570.1270.2470.87699.9
1.5-1.543.70.17551540.970.1050.2050.911100
1.54-1.593.70.15552050.9730.0930.1810.986100
1.59-1.643.70.13751730.9780.0820.161.098100
1.64-1.73.70.11951850.9820.0720.141.116100
1.7-1.763.70.09852090.9870.0590.1151.10499.9
1.76-1.843.80.08151690.990.0490.0951.05899.8
1.84-1.943.80.06951950.9920.0420.0810.99499.8
1.94-2.063.70.06252320.9920.0380.0731.0299.9
2.06-2.223.60.06151680.9920.0380.0721.12899.8
2.22-2.453.60.05551950.9930.0340.0650.96199.8
2.45-2.83.60.0552240.9950.0310.0590.80999.6
2.8-3.533.60.04652040.9950.0290.0540.68199.1
3.53-403.40.04449730.9930.0290.0530.60493.2

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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: 1.3→40 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.885 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2003 4735 5 %RANDOM
Rwork0.1484 ---
obs0.151 90448 91.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.54 Å2 / Biso mean: 18.319 Å2 / Biso min: 8.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0.19 Å2
2--0.07 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 5 592 3938
Biso mean--21.98 28.14 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0360.023590
X-RAY DIFFRACTIONr_bond_other_d0.0030.023239
X-RAY DIFFRACTIONr_angle_refined_deg2.9951.954913
X-RAY DIFFRACTIONr_angle_other_deg1.40637519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.645471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57223.841138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37115578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1381517
X-RAY DIFFRACTIONr_chiral_restr0.2110.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0214155
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02820
X-RAY DIFFRACTIONr_rigid_bond_restr7.43136828
X-RAY DIFFRACTIONr_sphericity_free18.5065382
X-RAY DIFFRACTIONr_sphericity_bonded9.49256941
LS refinement shellResolution: 1.3→1.332 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.23 116 -
Rwork0.188 2391 -
obs--32.84 %

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