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- PDB-7t0k: Crystal structure of S25-2 Fab Unliganded 4 -

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Basic information

Entry
Database: PDB / ID: 7t0k
TitleCrystal structure of S25-2 Fab Unliganded 4
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 / IODIDE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 9, 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,01542
Polymers193,7008
Non-polymers4,31534
Water7,008389
1
L: S25-2 Fab light chain
H: S25-2 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,69412
Polymers48,4252
Non-polymers1,26910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-27 kcal/mol
Surface area19890 Å2
MethodPISA
2
A: S25-2 Fab light chain
B: S25-2 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1868
Polymers48,4252
Non-polymers7616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-25 kcal/mol
Surface area19630 Å2
MethodPISA
3
C: S25-2 Fab light chain
D: S25-2 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,56711
Polymers48,4252
Non-polymers1,1429
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-26 kcal/mol
Surface area19440 Å2
MethodPISA
4
E: S25-2 Fab light chain
F: S25-2 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,56711
Polymers48,4252
Non-polymers1,1429
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-27 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.558, 135.497, 73.977
Angle α, β, γ (deg.)90.000, 94.260, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11L
21A
12L
22C
13L
23E
14H
24B
15H
25D
16H
26F
17A
27C
18A
28E
19B
29D
110B
210F
111C
211E
112D
212F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010L1 - 217
2010A1 - 217
1020L1 - 218
2020C1 - 218
1030L1 - 217
2030E1 - 217
1040H1 - 222
2040B1 - 222
1050H1 - 222
2050D1 - 222
1060H1 - 222
2060F1 - 222
1070A1 - 217
2070C1 - 217
1080A1 - 219
2080E1 - 219
1090B1 - 221
2090D1 - 221
10100B1 - 222
20100F1 - 222
10110C1 - 217
20110E1 - 217
10120D1 - 222
20120F1 - 222

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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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: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium iodide, 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→40 Å / Num. obs: 122420 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.054 / Rrim(I) all: 0.107 / Χ2: 1.332 / Net I/σ(I): 9.2 / Num. measured all: 502071
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.034.20.6960730.830.3880.7930.886100
2.03-2.074.20.59561020.8420.3350.6840.926100
2.07-2.114.20.52661610.8550.2950.6040.983100
2.11-2.154.20.45960600.8880.2570.5271.026100
2.15-2.24.20.41261240.910.230.4731.071100
2.2-2.254.20.36761370.9240.2050.4211.16100
2.25-2.314.20.33761100.920.1890.3871.175100
2.31-2.374.20.31161310.9360.1740.3571.257100
2.37-2.444.20.2760950.9520.1510.311.358100
2.44-2.524.20.23161180.9620.130.2661.503100
2.52-2.614.20.19961250.9670.1120.2291.52100
2.61-2.714.20.16861040.9720.0950.1941.594100
2.71-2.844.20.14361400.9810.0820.1651.653100
2.84-2.994.10.11961190.9860.0680.1371.73799.9
2.99-3.1740.09961170.9890.0580.1151.827100
3.17-3.423.90.08461450.990.050.0991.66399.9
3.42-3.763.80.07161200.9920.0430.0831.50899.6
3.76-4.313.80.06261230.9930.0370.0721.32199.4
4.31-5.423.80.05461280.9940.0320.0631.30799.3
5.42-403.90.0561880.9960.0290.0581.23398.9

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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: 1Q9K

1q9k


Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.91 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 6135 5 %RANDOM
Rwork0.2216 ---
obs0.2232 116254 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.75 Å2 / Biso mean: 44.563 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-3.05 Å20 Å20.25 Å2
2---3.43 Å20 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13480 0 34 389 13903
Biso mean--46.06 39.82 -
Num. residues----1752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213827
X-RAY DIFFRACTIONr_bond_other_d0.0060.0212606
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.94518804
X-RAY DIFFRACTIONr_angle_other_deg1.18329158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59751742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12423.779553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94152226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7731571
X-RAY DIFFRACTIONr_chiral_restr0.090.22108
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115565
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023146
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11L120540.09
12A120540.09
21L121980.09
22C121980.09
31L120660.09
32E120660.09
41H117540.09
42B117540.09
51H118060.08
52D118060.08
61H115760.08
62F115760.08
71A121500.09
72C121500.09
81A122270.09
82E122270.09
91B121890.08
92D121890.08
101B118530.09
102F118530.09
111C121250.09
112E121250.09
121D118630.08
122F118630.08
LS refinement shellResolution: 2.005→2.057 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 453 -
Rwork0.299 8339 -
all-8792 -
obs--96.79 %

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