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- PDB-7tqa: Crystal Structure of monoclonal S9.6 Fab -

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Basic information

Entry
Database: PDB / ID: 7tqa
TitleCrystal Structure of monoclonal S9.6 Fab
Components
  • Fab S9.6 heavy chain
  • Fab S9.6 light chain
KeywordsIMMUNE SYSTEM / Antibody / Fab / DNA-RNA hybrid / Nucleic Acid binding protein / ribonucleoprotein complex
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.328 Å
AuthorsBou-Nader, C. / Zhang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis of R-loop recognition by the S9.6 monoclonal antibody.
Authors: Bou-Nader, C. / Bothra, A. / Garboczi, D.N. / Leppla, S.H. / Zhang, J.
History
DepositionJan 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 15, 2023Group: Data collection / Structure summary / Category: audit_author / chem_comp_atom / chem_comp_bond / Item: _audit_author.name
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab S9.6 heavy chain
L: Fab S9.6 light chain
C: Fab S9.6 heavy chain
D: Fab S9.6 light chain
A: Fab S9.6 heavy chain
B: Fab S9.6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,53819
Polymers147,2936
Non-polymers1,24513
Water7,530418
1
H: Fab S9.6 heavy chain
L: Fab S9.6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3865
Polymers49,0982
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-66 kcal/mol
Surface area18570 Å2
MethodPISA
2
C: Fab S9.6 heavy chain
D: Fab S9.6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4786
Polymers49,0982
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-73 kcal/mol
Surface area19190 Å2
MethodPISA
3
A: Fab S9.6 heavy chain
B: Fab S9.6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6748
Polymers49,0982
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-90 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.649, 96.649, 140.583
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Antibody Fab S9.6 heavy chain


Mass: 24972.879 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab S9.6 light chain


Mass: 24124.740 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 50 mM Bis-Tris, 24% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.328→45.7 Å / Num. obs: 62725 / % possible obs: 99.57 % / Redundancy: 14.6 % / CC1/2: 0.996 / Net I/σ(I): 9.24
Reflection shellResolution: 2.328→2.411 Å / Mean I/σ(I) obs: 1.55 / Num. unique obs: 6284 / CC1/2: 0.522 / % possible all: 99.35

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: OTHER PDB DEPOSITION IN THIS WORK

Resolution: 2.328→45.7 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 2897 4.62 %
Rwork0.1794 59790 -
obs0.182 62687 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.38 Å2 / Biso mean: 47.1695 Å2 / Biso min: 21.5 Å2
Refinement stepCycle: final / Resolution: 2.328→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9780 0 74 418 10272
Biso mean--109.92 46.45 -
Num. residues----1297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.328-2.36580.34371240.2664284598
2.3658-2.40660.33361300.25932880100
2.4066-2.45030.2881500.2485277099
2.4503-2.49750.34911410.2417282398
2.4975-2.54840.28061740.22982852100
2.5484-2.60390.3251300.23122882100
2.6039-2.66440.28651360.21782849100
2.6644-2.7310.26051820.20822763100
2.731-2.80490.28691460.21022889100
2.8049-2.88740.27291310.20692852100
2.8874-2.98060.24771080.19712905100
2.9806-3.08710.2741100.19442862100
3.0871-3.21070.27321560.19722862100
3.2107-3.35670.23791480.19562866100
3.3567-3.53360.26121140.19112796100
3.5336-3.75490.24641010.1643287598
3.7549-4.04470.20751740.15662860100
4.0447-4.45140.17661400.13592820100
4.4514-5.09480.1681380.13442886100
5.0948-6.41610.20871180.1652871100
6.4161-45.70.21051460.1654278298
Refinement TLS params.Method: refined / Origin x: 64.0163 Å / Origin y: -53.8581 Å / Origin z: 2.2483 Å
111213212223313233
T0.3218 Å20.005 Å20.0422 Å2-0.3051 Å20.0035 Å2--0.3091 Å2
L0.0593 °20.0117 °2-0.0157 °2--0.0943 °20.0392 °2--0.0304 °2
S-0.0215 Å °0.0532 Å °-0.0292 Å °-0.0241 Å °-0.0197 Å °-0.0238 Å °0.0337 Å °-0.0602 Å °0.0387 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH1 - 214
2X-RAY DIFFRACTION1allH215 - 290
3X-RAY DIFFRACTION1allL1 - 276
4X-RAY DIFFRACTION1allC1 - 284
5X-RAY DIFFRACTION1allD1 - 280
6X-RAY DIFFRACTION1allA1 - 218
7X-RAY DIFFRACTION1allA219 - 283
8X-RAY DIFFRACTION1allB1 - 219
9X-RAY DIFFRACTION1allB220 - 305
10X-RAY DIFFRACTION1allE1 - 25
11X-RAY DIFFRACTION1allF1

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