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- PDB-9udt: Single-chain Fv antibody of C6 complex with NNP-Cap -

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Basic information

Entry
Database: PDB / ID: 9udt
TitleSingle-chain Fv antibody of C6 complex with NNP-Cap
ComponentsSingle-chain Fv antibody of C6
KeywordsIMMUNE SYSTEM / ANTIGEN BINDING / AFFINITY MATURATION / SOMATIC HYPERMUTATION
Function / homology: / ACETATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsYoshida, M. / Hanazono, Y. / Numoto, N. / Ito, N. / Oda, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis of anti-(4-hydroxy-3-nitrophenyl)acetyl antibodies during affinity maturation
Authors: Yoshida, M. / Hanazono, Y. / Numoto, N. / Yabuno, S. / Ito, N. / Azuma, T. / Oda, M.
History
DepositionApr 7, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single-chain Fv antibody of C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5333
Polymers26,1171
Non-polymers4162
Water5,747319
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.148, 77.511, 82.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody Single-chain Fv antibody of C6


Mass: 26116.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-A1L81 / 6-[2-(3,5-dinitro-4-oxidanyl-phenyl)ethanoylamino]hexanoic acid


Mass: 357.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N3O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate pH 6.5, 20% w/v polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.08→50 Å / Num. obs: 106239 / % possible obs: 99.5 % / Redundancy: 25.4 % / Biso Wilson estimate: 8.37 Å2 / Rmerge(I) obs: 0.286 / Net I/σ(I): 22.2
Reflection shellResolution: 1.08→1.11 Å / Redundancy: 20.7 % / Rmerge(I) obs: 3.084 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 10008 / CC1/2: 0.691 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.08→36.42 Å / SU ML: 0.1358 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.9088
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1678 5295 4.99 %
Rwork0.1514 100851 -
obs0.1522 106146 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.31 Å2
Refinement stepCycle: LAST / Resolution: 1.08→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 29 319 2099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862144
X-RAY DIFFRACTIONf_angle_d1.08162957
X-RAY DIFFRACTIONf_chiral_restr0.0936327
X-RAY DIFFRACTIONf_plane_restr0.0107382
X-RAY DIFFRACTIONf_dihedral_angle_d13.6095800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.090.52221470.52282868X-RAY DIFFRACTION85.22
1.09-1.10.39061550.41793267X-RAY DIFFRACTION97.58
1.1-1.110.32361760.30623323X-RAY DIFFRACTION99.4
1.11-1.130.22191890.22553329X-RAY DIFFRACTION99.91
1.13-1.140.19151690.17953321X-RAY DIFFRACTION99.89
1.14-1.160.21551830.16953374X-RAY DIFFRACTION99.89
1.16-1.180.21071740.16963304X-RAY DIFFRACTION99.91
1.18-1.190.18951790.17943411X-RAY DIFFRACTION100
1.19-1.210.20821730.20023306X-RAY DIFFRACTION100
1.21-1.230.21511730.21623370X-RAY DIFFRACTION99.92
1.23-1.250.26471640.22953335X-RAY DIFFRACTION99.97
1.25-1.280.24061870.19093363X-RAY DIFFRACTION99.97
1.28-1.30.1721800.1663334X-RAY DIFFRACTION100
1.3-1.330.16081840.14513344X-RAY DIFFRACTION99.97
1.33-1.360.17861670.13513378X-RAY DIFFRACTION99.94
1.36-1.390.17371750.13073349X-RAY DIFFRACTION99.97
1.39-1.420.15221890.1283373X-RAY DIFFRACTION100
1.42-1.460.17221630.12583361X-RAY DIFFRACTION100
1.46-1.50.16231780.13083370X-RAY DIFFRACTION99.97
1.5-1.550.14441790.13043398X-RAY DIFFRACTION99.97
1.55-1.610.16281730.12733371X-RAY DIFFRACTION99.97
1.61-1.670.14391870.12043360X-RAY DIFFRACTION100
1.67-1.750.14321840.12433405X-RAY DIFFRACTION100
1.75-1.840.15171700.12823410X-RAY DIFFRACTION100
1.84-1.950.14761830.12393383X-RAY DIFFRACTION100
1.95-2.110.14551800.12383423X-RAY DIFFRACTION100
2.11-2.320.15251840.13563416X-RAY DIFFRACTION100
2.32-2.650.16241800.14823452X-RAY DIFFRACTION100
2.65-3.340.16521840.14863490X-RAY DIFFRACTION100
3.34-36.420.14361860.15883663X-RAY DIFFRACTION99.92

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