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- PDB-8kgz: Crystal structure of single-chain Fv antibody against antigen pep... -

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Basic information

Entry
Database: PDB / ID: 8kgz
TitleCrystal structure of single-chain Fv antibody against antigen peptide from SARS-CoV2 S-spike protein
ComponentsThioredoxin 1,scFv
KeywordsIMMUNE SYSTEM / ScFv / antibody / S-spike protein / antigen
Function / homology
Function and homology information


DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytosol / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsMa, Q.Q. / Zhang, B.L. / Cheng, X.Y. / Huang, Y.Q. / Su, Z.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of sheep scFv antibody against an antigen peptide of SARS-CoV2 S-spike protein
Authors: Ma, Q.Q. / Zheng, B.L. / Cheng, X.Y. / Huang, Y.Q. / Su, Z.D.
History
DepositionAug 20, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin 1,scFv
B: Thioredoxin 1,scFv


Theoretical massNumber of molelcules
Total (without water)86,3982
Polymers86,3982
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.210, 77.753, 61.346
Angle α, β, γ (deg.)90.00, 112.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Thioredoxin 1,scFv / Trx-1


Mass: 43198.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Ovis aries (sheep)
Gene: trxA, fipA, tsnC, b3781, JW5856 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA25
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.54 Å3/Da / Density % sol: 20.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.1M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.21→77.75 Å / Num. obs: 179188 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.882 / Net I/σ(I): 4.1
Reflection shellResolution: 2.21→2.27 Å / Redundancy: 6.4 % / Num. unique obs: 26361 / CC1/2: 0.882

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata scaling
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→55.79 Å / Cor.coef. Fo:Fc: 0.836 / Cor.coef. Fo:Fc free: 0.761 / SU B: 11.927 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32114 1227 4.7 %RANDOM
Rwork0.26886 ---
obs0.27129 25094 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.916 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20.1 Å2
2--1.23 Å2-0 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 2.21→55.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 0 104 3483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0113774
X-RAY DIFFRACTIONr_bond_other_d0.0030.0163450
X-RAY DIFFRACTIONr_angle_refined_deg1.931.6445138
X-RAY DIFFRACTIONr_angle_other_deg0.6671.5647940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8215502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.03520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.30410562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024534
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02866
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.842.7182026
X-RAY DIFFRACTIONr_mcbond_other4.7172.7152026
X-RAY DIFFRACTIONr_mcangle_it8.0014.8372522
X-RAY DIFFRACTIONr_mcangle_other8.0174.8472523
X-RAY DIFFRACTIONr_scbond_it4.8042.9181748
X-RAY DIFFRACTIONr_scbond_other4.8032.9261749
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.6865.3382617
X-RAY DIFFRACTIONr_long_range_B_refined38.45461.074159
X-RAY DIFFRACTIONr_long_range_B_other38.45361.14160
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 88 -
Rwork0.406 1852 -
obs--99.9 %

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