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- PDB-6k4z: Single-chain Fv antibody of C6 COMPLEXED WITH 2-(4-HYDROXY-3-NITR... -

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Basic information

Entry
Database: PDB / ID: 6k4z
TitleSingle-chain Fv antibody of C6 COMPLEXED WITH 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID
ComponentsscFv of C6
KeywordsIMMUNE SYSTEM / antigen binding / affinity maturation / Somatic hypermutation / conformational change
Function / homology2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNishiguchi, A. / Numoto, N. / Ito, N. / Azuma, T. / Oda, M.
CitationJournal: Mol.Immunol. / Year: 2019
Title: Three-dimensional structure of a high affinity anti-(4-hydroxy-3-nitrophenyl)acetyl antibody possessing a glycine residue at position 95 of the heavy chain.
Authors: Nishiguchi, A. / Numoto, N. / Ito, N. / Azuma, T. / Oda, M.
History
DepositionMay 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 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
A: scFv of C6
B: scFv of C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8166
Polymers52,2342
Non-polymers5824
Water9,764542
1
A: scFv of C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5024
Polymers26,1171
Non-polymers3853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10480 Å2
MethodPISA
2
B: scFv of C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3142
Polymers26,1171
Non-polymers1971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.393, 46.779, 74.581
Angle α, β, γ (deg.)88.235, 103.780, 111.984
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Antibody scFv of C6


Mass: 26116.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The fusion protein of expression tags (residues -2-0), the light chain (residues 1-108), linker GGGGSGGGGSGGGGS (residues 501-515), and the heavy chain (residues 1001-1113)
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET-32TH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): codon plus
#2: Chemical ChemComp-NPA / 2-(4-HYDROXY-3-NITROPHENYL)ACETIC ACID


Mass: 197.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / 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.: 542 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.14 M Lithium sulfate monohydrate, 0.07 M TRIS hydrochloride pH 8.5, 21% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 12, 2018
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 52628 / % possible obs: 96.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.07 Å2 / CC1/2: 0.998 / Rsym value: 0.073 / Net I/σ(I): 11.2
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 3.5 % / Num. unique obs: 8339 / CC1/2: 0.716 / Rsym value: 0.586 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Cootmodel building
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ET9

3et9


Resolution: 1.65→43.29 Å / SU ML: 0.173 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.1576
RfactorNum. reflection% reflection
Rfree0.1956 2600 4.94 %
Rwork0.1674 --
obs0.1689 52622 96.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.58 Å2
Refinement stepCycle: LAST / Resolution: 1.65→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 39 542 4067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00683642
X-RAY DIFFRACTIONf_angle_d0.8654978
X-RAY DIFFRACTIONf_chiral_restr0.0581544
X-RAY DIFFRACTIONf_plane_restr0.0055629
X-RAY DIFFRACTIONf_dihedral_angle_d16.10732118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.29881310.26742555X-RAY DIFFRACTION93.59
1.68-1.710.2861160.2562638X-RAY DIFFRACTION94.48
1.71-1.750.28491320.24142566X-RAY DIFFRACTION94.2
1.75-1.790.25711430.22772615X-RAY DIFFRACTION94.45
1.79-1.830.27231160.21842528X-RAY DIFFRACTION94.26
1.83-1.870.26381460.20622638X-RAY DIFFRACTION95.38
1.87-1.920.23871430.19732581X-RAY DIFFRACTION95.28
1.92-1.980.21491260.182649X-RAY DIFFRACTION95.69
1.98-2.040.20241370.16382598X-RAY DIFFRACTION95.76
2.04-2.120.18671410.16072659X-RAY DIFFRACTION96.62
2.12-2.20.18851260.16052647X-RAY DIFFRACTION96.65
2.2-2.30.23951390.16952627X-RAY DIFFRACTION96.98
2.3-2.420.22581470.17072670X-RAY DIFFRACTION97.24
2.42-2.570.20941440.17122652X-RAY DIFFRACTION97.46
2.57-2.770.17251370.16772684X-RAY DIFFRACTION97.82
2.77-3.050.21141400.16582669X-RAY DIFFRACTION98.11
3.05-3.490.14811460.15042685X-RAY DIFFRACTION98.13
3.49-4.40.15951540.13152685X-RAY DIFFRACTION98.44
4.4-43.30.16751360.15112676X-RAY DIFFRACTION97.57

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